Case 11 (XFP): Denmark/DCGC-692222/2025


Target: 9 samples Number of changes: 146
BC: LF.7.9 + A.2.5.1 + LF.7.9BC BR: 134-135, 136-137 BC BR coord: 27810 - 27811, 28145 - 28146
Direction L1: >> Initial region span: 1-134,135-136,141-146Gap history (edge excluded): 134-141 -> 136-141
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.93e-02
Rec. model vs L1: 2.89e-16 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

LF.7.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.9 20 134 204.080142 NaN NaN NaN * * *
XFJ.3 14 116 203.689067 190.056827 -42.113654 5.829466e-05 *
XFJ.1 59 116 203.361657 194.696687 -51.393374 6.036083e-03 *
JN.1.4 8971 134 166.141072 176.399125 -14.798251 6.844436e-11 *
LF.7 58 134 153.506696 149.378940 39.242120 1.260958e-22 *
JN.1 17255 134 143.567535 152.644170 32.711659 3.301203e-21 *
LF.7.2.1 67 134 140.394377 147.541603 42.916795 2.002622e-23 *
LF.7.1 165 135 137.220118 144.581697 48.836606 1.037737e-24 *
LF.7.9.1 48 134 136.458760 132.349838 73.300323 5.066006e-30 *
LF.7.1.2 26 134 133.802412 129.762335 78.475331 3.800520e-31 *
|||||

A.2.5.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
A.2.5.1 25 136 8.760478 NaN NaN NaN * * *
A.2.5 513 136 6.835739 6.835739 -9.671479 0.145876 * *
B.1.1.149 55 135 5.220104 -4.779896 13.559792 0.000001 *
CH.1.1.9 97 135 5.220104 -4.779896 13.559792 0.000001 *
CH.1.1.13 145 135 5.213183 -4.786817 13.573633 0.000001 *
CH.1.1.14 88 135 5.197114 -4.802886 13.605771 0.000001 *
AY.62 1056 135 5.193231 -4.806769 13.613538 0.000001 *
BR.2.1 313 135 5.190928 -4.809072 13.618143 0.000001 *
NL.18 10 135 5.114743 -4.885257 13.770513 0.000001 *
MC.2 396 140 5.113976 2.501432 -1.002865 0.001911 *
|||||

LF.7.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.9 20 141 7.496435 None None None * * *



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 11 (XFP): OZ285414


Target: 9 samples Number of changes: 151
BC: XFJ.1 + MC.2 BC BR: 119-120 BC BR coord: 25216 - 25217
Direction L1: >> Initial region span: 1-119,123-151Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.89e-02
Rec. model vs L1: 1.18e-60Rec. model vs L2: 3.06e-139
Flags: Model_1BP_Best

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 119 181.384545 NaN NaN NaN * * *
LF.7.9 20 137 177.626648 168.600273 -41.200547 2.802496e-06
XFJ.3 14 119 168.317700 168.317700 -40.635400 2.118081e-06 *
JN.1 17255 137 148.474683 120.641301 54.717397 4.157016e-27
JN.1.4 8971 137 146.200272 118.757915 58.484170 6.343195e-28
PY.1 82 119 134.256585 134.256585 27.486830 3.401740e-21 *
LF.7 58 137 128.987966 119.573868 56.852265 1.433039e-27
LF.7.9.3 20 107 128.180951 124.377896 47.244208 1.750020e-25
KP.2.3 4440 137 120.509237 107.334479 81.331041 6.926177e-33
JN.1.16.1 466 138 120.276038 110.810640 74.378720 2.237005e-31
|||||

MC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.2 396 123 44.449423 NaN NaN NaN * * *
KP.3.1.1 12013 121 35.668647 35.395693 -2.791385 2.650265e+04 *
JN.1.20 66 123 35.429427 16.191774 35.616452 1.209661e-04 * *
KP.3.1 1957 123 32.321589 13.083937 41.832127 5.422248e-06 *
MC.10 221 123 31.699491 12.461839 43.076322 2.902320e-06 *
KP.3 769 120 31.389966 31.389966 5.220068 4.829920e+02 *
MC.19 221 123 31.343269 12.105617 43.788767 2.035030e-06 *
NY.15 216 123 30.529708 -2.347172 72.694345 1.078985e-12 *
MC.16 917 123 29.278353 10.040700 47.918600 2.580790e-07 *
JN.1.46 308 121 28.922346 18.922346 30.155309 1.854760e-03 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14371_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 15783_C|T,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 11 (XFP): USA/CA-GBW-GKISBBBE89075/2025


Target: 9 samples Number of changes: 149
BC: KP.2.28.1 + XFJ.1 BC BR: 12-13 BC BR coord: 5240 - 5241
Direction L1: << Initial region span: 1-8,13-149Gap history (edge excluded): 8-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.71e-02
Rec. model vs L1: 1.61e-129Rec. model vs L2: 2.57e-25
Flags: Model_1BP_Best

KP.2.28.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.28.1 10 8 18.811150 NaN NaN NaN * * *
LP.1 659 11 17.020940 1.332105 27.335791 1.447735 *
LF.1.1.1 109 8 16.348047 -10.543103 51.086206 0.000010 * *
BA.2.86.1 1343 11 16.191494 6.191494 17.617013 186.792804 *
KP.3.1.1 12013 11 15.885304 5.885304 18.229391 137.689342 *
JN.1.31 204 8 15.720993 -2.132149 34.264297 0.045502 * *
KP.3.1 1957 8 15.233281 -2.623443 35.246886 0.027737 * *
KP.2.3 4440 11 13.894198 3.894198 22.211604 18.821503 *
JN.1.39 1007 11 10.874362 0.874362 28.251276 0.918512 *
MG.1 23 11 8.835060 -1.164940 32.329880 0.119433 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 13 195.146903 NaN NaN NaN * * *
LF.7.9 20 25 176.417928 172.803235 -21.606470 1.985461e-10
XFJ.3 14 13 172.658536 172.658536 -21.317072 1.717468e-10 *
JN.1.4 8971 5 164.445377 152.584793 18.830415 3.284179e-19
LF.7.1 165 25 155.105209 145.815757 32.368487 3.769235e-22
PY.2 17 25 149.216202 136.978220 50.043560 5.486071e-26
LF.7 58 25 144.019777 140.387692 43.224616 1.660373e-24
LF.7.2.1 67 25 143.102115 139.487422 45.025155 6.716904e-25
LF.7.6.2 17 25 136.675995 133.061302 57.877395 1.088497e-27
PY.1 82 25 136.662298 124.114296 75.771407 1.419263e-31



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23230_C|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 11 (XFP): USA/MA-MASPHL-14151/2025


Target: 9 samples Number of changes: 154
BC: MC.11 + XFJ.1 BC BR: 17-18 BC BR coord: 5240 - 5241
Direction L1: << Initial region span: 1-11,18-154Gap history (edge excluded): 11-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.45e-02
Rec. model vs L1: 3.93e-154Rec. model vs L2: 2.20e-30
Flags: Model_1BP_Best

MC.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.11 393 11 22.372168 NaN NaN NaN * * *
LB.1 1128 12 21.979768 -5.874261 49.748522 1.491317e+04 * *
LB.1.7.2 87 11 13.599679 -30.758253 99.516507 2.323549e-07 *
KP.2.8 51 6 13.418012 -26.240827 90.481654 2.133845e-05 *
JN.1.42.2 28 6 13.024106 -26.548115 91.096230 1.565062e-05 *
MC.10.1.7 11 6 12.932207 -31.500739 101.001478 1.108597e-07
JN.1.30 57 12 12.876348 -14.976794 67.953588 1.665291e+00 * *
MH.1 51 6 12.808788 -26.808743 91.617486 1.206744e-05 *
JN.1.15 42 11 12.200034 -25.653108 89.306216 3.830232e-05 * *
KS.1.1.2 252 13 11.998422 -5.854720 49.709441 1.521444e+04 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 18 180.312387 NaN NaN NaN * * *
LF.7.9 20 30 176.417928 172.803235 -35.606470 5.503259e-04 *
XFJ.3 14 18 172.658536 172.658536 -35.317072 4.760441e-04 * *
JN.1.4 8971 15 151.567214 148.522050 12.955900 1.562350e-14
JN.1 17255 18 141.621231 141.621231 26.757538 1.574514e-17 *
LF.7.1 165 30 140.788276 131.498824 47.002353 6.339957e-22
LF.7.9.1 48 30 135.667219 123.429237 63.141525 1.983033e-25
PY.2 17 30 134.235975 121.997992 66.004015 4.745574e-26
LF.7 58 30 129.168167 125.536082 58.927836 1.627495e-24
LF.7.2.1 67 30 128.107073 124.492380 61.015240 5.723768e-25



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2003_C|T, 2036_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 3924_C|T, 3964_A|G, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16741_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 20796_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29734_29759

Case 11 (XFP): USA/NJ-GBW-GKISBBBF09579/2025


Target: 9 samples Number of changes: 152
BC: MC.17.1 + XFJ.1 BC BR: 17-18 BC BR coord: 5240 - 5241
Direction L1: << Initial region span: 1-6,18-152Gap history (edge excluded): 6-18
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.65e-182Rec. model vs L2: 5.83e-26
Flags: Model_2BP_Bad_L1_opp

MC.17.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.17.1 10 6 16.193570 NaN NaN NaN * * *
KP.3.2.5 93 6 13.633444 -41.161875 126.323750 2.035376e-08 *
MC.9 298 6 12.481026 -16.429015 76.858029 1.118787e+03 * *
MC.28.1.1 129 6 9.974781 -29.568854 103.137708 2.198456e-03 * *
KP.2.3 4440 6 9.784386 -10.767208 65.534415 3.228684e+05 * *
KP.3.1.1 12013 6 8.740606 -12.024975 68.049950 9.158291e+04 * *
JN.1 17255 6 6.960903 -6.647399 57.294798 1.987553e+07 * *
JN.1.4 8971 5 6.391498 -4.224472 52.448944 2.235174e+08 * *
BA.2.6 424 5 3.268319 -73.506090 191.012180 1.825533e-22 *
FL.2.3 614 3 2.883722 -74.648894 193.297789 5.809283e-23
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 18 188.148415 NaN NaN NaN * * *
LF.7.9 20 30 183.528825 179.914132 -43.828264 2.652070e-04 *
XFJ.3 14 18 181.358668 181.358668 -46.717337 1.124969e-03 * *
JN.1.4 8971 9 165.815847 154.198007 7.603986 1.801782e-15
LF.7.1 165 30 147.236797 137.947345 40.105310 1.571251e-22
LF.7.9.1 48 30 142.102988 129.865006 56.269988 4.865709e-26
PY.2 17 30 140.933038 128.695056 58.609887 1.510155e-26
LF.7.9.3 20 30 139.066797 129.102994 57.794013 2.275529e-26
LF.7 58 30 135.678767 132.046682 51.906635 4.304355e-25
LF.7.2.1 67 30 134.709279 131.094586 53.810828 1.664671e-25



Target sequence

, 21_C|T, 44_C|T, 198_G|A, 241_C|T, 670_T|G, 897_C|A, 1636_G|C, 2135_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 5192_C|T, 6183_A|G, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22991_A|G, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 11 (XFP): USA/NY-GBW-GKISBBBE99208/2025


Target: 9 samples Number of changes: 151
BC: XFJ.1 + MC.13 BC BR: 120-121 BC BR coord: 25216 - 25217
Direction L1: >> Initial region span: 1-120,124-151Gap history (edge excluded): 120-124
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.32e-45 Rec. model vs L2: 8.98e-170
Flags: Model_2BP_Bad_L1_opp

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 120 207.715389 NaN NaN NaN * * *
XFJ.3 14 120 193.289360 193.289360 -106.578720 5.436284e-07 *
LF.7.9 20 138 189.949082 180.922708 -81.845416 2.318733e-12
JN.1.4 8971 138 167.226103 139.783746 0.432507 3.150474e-30
LF.7 58 138 158.650769 149.236671 -18.473342 4.003674e-26
JN.1 17255 138 145.582746 117.749364 44.501271 8.485881e-40
LF.7.2.1 67 138 145.143356 135.707994 8.584012 5.353352e-32
KP.2.3 4440 138 141.800275 128.625518 22.748964 4.483833e-35
LF.7.1 165 139 141.496991 131.908981 16.182039 1.197586e-33
LF.7.1.2 26 138 139.200545 129.677247 20.645505 1.281323e-34
|||||

MC.13 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.13 807 124 32.600488 NaN NaN NaN * * *
JN.1.7.5 427 122 31.495733 14.388791 41.222418 2.787095e+00 *
MC.2 396 124 31.383899 12.146246 45.707507 2.952302e-01 * *
KP.3.1 1957 124 28.117999 8.880347 52.239306 1.127689e-02 * *
KP.3.1.1 12013 122 26.714901 26.441947 17.116106 4.768704e+05 *
JN.1.42 494 124 23.359133 4.121480 61.757040 9.659341e-05 * *
LB.1.3.2 390 124 23.315157 -2.179318 74.358636 1.773749e-07 *
JN.1.4.5 1757 124 22.606494 3.368273 63.263454 4.562750e-05 * *
LB.1 1128 121 21.952824 21.952824 26.094351 5.377614e+03 *
JN.1.46 308 122 21.020620 11.020620 47.958761 9.584720e-02 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29789_29790

Case 11 (XFP): USA/NY-GBW-GKISBBBE99384/2025


Target: 9 samples Number of changes: 150
BC: XFJ.3 + MC.13 BC BR: 119-120 BC BR coord: 25216 - 25217
Direction L1: >> Initial region span: 1-119,123-150Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.02e-47 Rec. model vs L2: 2.13e-163
Flags: Model_2BP_Bad_L1_opp

XFJ.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.3 14 119 189.742002 NaN NaN NaN * * *
XFJ.1 59 119 189.367704 189.367704 -92.735408 6.907343e-01 * *
LF.7.9 20 137 186.401724 177.375350 -68.750700 4.265292e-06
JN.1.4 8971 137 161.828990 134.386633 17.226734 9.112320e-25
JN.1 17255 137 140.350729 112.517347 60.965305 2.894734e-34
LF.7 58 137 140.286584 130.872487 24.255027 2.710715e-26
KP.2.3 4440 137 134.856598 121.681841 42.636318 2.766416e-30
LF.7.2.1 67 137 126.600956 117.165593 51.668814 3.027457e-32
LF.7.9.3 20 137 125.528831 122.916078 40.167845 9.511987e-30
LF.7.1 165 138 123.657091 114.069080 57.861840 1.370682e-33
|||||

MC.13 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.13 807 123 32.600488 NaN NaN NaN * * *
JN.1.7.5 427 121 31.495733 14.388791 41.222418 2.787095e+00 *
MC.2 396 123 31.383899 12.146246 45.707507 2.952302e-01 * *
KP.3.1 1957 123 28.117999 8.880347 52.239306 1.127689e-02 * *
KP.3.1.1 12013 121 26.714901 26.441947 17.116106 4.768704e+05 *
JN.1.42 494 123 23.359133 4.121480 61.757040 9.659341e-05 * *
LB.1.3.2 390 123 23.315157 -2.179318 74.358636 1.773749e-07 *
JN.1.4.5 1757 123 22.606494 3.368273 63.263454 4.562750e-05 * *
LB.1 1128 120 21.952824 21.952824 26.094351 5.377614e+03 *
JN.1.46 308 121 21.020620 11.020620 47.958761 9.584720e-02 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2172_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21995_21997, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29789_29790

Case 11 (XFP): USA/NY-GBW-GKISBBBF41177/2025


Target: 9 samples Number of changes: 150
BC: XFJ.3 + KP.3.1 BC BR: 119-120 BC BR coord: 25216 - 25217
Direction L1: >> Initial region span: 1-119,123-150Gap history (edge excluded): 119-123
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 7.95e-09
Rec. model vs L1: 3.48e-47Rec. model vs L2: 5.92e-98
Flags: Model_1BP_Best

XFJ.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.3 14 119 180.460350 NaN NaN NaN * * *
XFJ.1 59 119 179.256731 179.256731 -64.513463 2.996920e-01 * *
LF.7.9 20 137 175.530838 166.504463 -39.008926 8.698022e-07
JN.1.4 8971 138 154.716590 126.066787 41.866426 2.379861e-24
JN.1 17255 137 146.673059 118.839678 56.320645 1.732902e-27
LF.7.9.3 20 111 132.756853 124.934294 44.131412 7.687744e-25
KP.2.3 4440 138 131.980467 118.341840 57.316320 1.051058e-27
LF.7 58 137 128.850800 119.436702 55.126596 3.141805e-27
LF.7.9.1 48 111 117.731415 109.908855 74.182289 2.293635e-31
JN.1.16.1 466 137 116.962133 107.671266 78.657468 2.441769e-32
|||||

KP.3.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1 1957 123 38.014816 NaN NaN NaN * * *
KP.3.1.1 12013 121 35.490289 35.217335 -4.434669 1.379753e+07 *
LB.1 1128 120 35.345047 35.345047 -4.690094 1.571302e+07 *
MC.6 366 123 32.529829 13.292177 39.415647 4.148535e-03 * *
JN.1.7.5 427 121 31.495733 14.388791 37.222418 1.246289e-02 *
MC.2 396 123 31.383899 12.146246 41.707507 1.320163e-03 * *
JN.1.4 8971 123 28.351818 27.105650 11.788700 4.146418e+03 * *
KP.2 1589 123 27.806551 8.568899 48.862202 3.698493e-05 * *
KP.2.3 4440 123 27.553370 11.997640 42.004721 1.141970e-03 * *
JN.1 17255 123 24.788840 24.026217 17.947565 1.905663e+02 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 4184_G|A, 4321_C|T, 4369_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10260_A|G, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13944_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23896_C|T, 23933_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A,
25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
27916_G|T, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 11 (XFP): IGS-10285-CVDP-7DC538F8-A098-480C-A770-7BD46A9127F9


Target: 9 samples Number of changes: 153
BC: JN.1.48 + XFJ.1 BC BR: 14-15 BC BR coord: 5240 - 5241
Direction L1: << Initial region span: 1-8,18-153Gap history (edge excluded): 8-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.71e-02
Rec. model vs L1: 2.36e-104Rec. model vs L2: 2.57e-25
Flags: Model_1BP_Best

JN.1.48 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.48 10 8 19.331200 NaN NaN NaN * * *
KP.2.2 1334 8 19.153903 -9.116624 48.233249 1.214897e+04 * *
JN.1.11.1 226 8 17.701017 -20.165488 70.330976 1.930126e-01 * *
LF.1.1.1 109 8 17.561244 -29.329905 88.659811 2.019652e-05 * *
KP.2 1589 9 17.523915 -10.334275 50.668550 3.586744e+03 * *
LB.1.3 778 9 16.123190 -11.732524 53.465048 8.844801e+02 * *
JN.1 17255 12 14.074274 3.940983 22.118035 5.678767e+09 *
KP.3.1 1957 8 13.961572 -23.895152 77.790304 4.630919e-03 * *
KP.2.3 4440 8 13.190259 -5.460208 40.920415 4.697707e+05 * *
KP.3.1.1 12013 8 12.183771 -15.791870 61.583740 1.533289e+01 * *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 18 176.702596 NaN NaN NaN * * *
LF.7.9 20 29 176.417928 152.803235 8.393530 5.503259e-04 *
XFJ.3 14 18 169.048745 152.658536 8.682928 4.760441e-04 * *
JN.1.4 8971 18 156.153465 139.759683 34.480634 1.189182e-09 *
LF.7.1 165 29 140.788276 111.498824 91.002353 6.339957e-22
LF.7.9.1 48 29 135.667219 103.429237 107.141525 1.983033e-25
PY.2 17 29 134.235975 101.997992 110.004015 4.745574e-26
LF.7 58 29 129.168167 105.536082 102.927836 1.627495e-24
JN.1 17255 18 128.113898 122.305365 69.389270 3.123476e-17 *
LF.7.2.1 67 29 128.107073 104.492380 105.015240 5.723768e-25



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2745_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3784_C|T, 3785_T|C, 4184_G|A, 4321_C|T, 4369_T|C, 4618_C|T, 6183_A|G, 6885_G|T, 7358_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10954_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18177_T|C, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20384_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25494_G|A, 25584_C|T, 25599_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28144_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29466_C|T, 29510_A|C, 29734_29759

Case 25 (XDY): USA/NY-PRL-250401_81E07/2025


Target: 220 samples Number of changes: 139
BC: XDY.6 + CK.2 BC BR: 134-135 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-134,135-139Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.18e-22 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

XDY.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XDY.6 11 134 237.235060 NaN NaN NaN * * *
XDY.5 17 134 237.107812 237.107812 -176.215624 8.824969e-01 * *
XDY.7 10 134 229.329634 229.329634 -160.659269 3.688944e-04 * *
LB.1.2.1 155 134 227.886172 227.886172 -157.772344 8.696542e-05 * *
XDY.3 16 134 207.303742 207.303742 -116.607483 1.003613e-13 *
LB.1.1 52 134 198.644565 198.644565 -99.289130 1.740107e-17 *
KP.2 1589 134 194.385261 194.385261 -90.770521 2.457432e-19 *
LB.1.3 778 134 191.696262 191.696262 -85.392523 1.668128e-20 *
KP.3.2 737 134 189.475062 189.475062 -80.950123 1.811739e-21 *
LB.1.2 199 134 189.410463 189.410463 -80.820926 1.697721e-21 *
|||||

CK.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
CK.2 112 135 13.286246 NaN NaN NaN * * *
KP.3.2.4 444 135 7.789327 7.789327 -5.578654 4.107256e-03 * *
BV.1 84 137 6.868162 -13.131838 36.263675 3.373737e-12
KP.3.2.3 759 136 6.782703 6.535354 -3.070709 1.170880e-03 * *
LF.7.1.6 14 137 6.514966 -13.485034 36.970069 2.365575e-12
BQ.1.25 479 136 6.009363 -3.990637 17.981274 3.144581e-08 *
XBB.1.5.89 23 137 5.870399 -14.129601 38.259203 1.241129e-12
BF.15 143 137 5.863296 -14.136704 38.273409 1.234938e-12
PD.2.1 10 137 5.619294 -14.380706 38.761412 9.665919e-13
CM.10 43 137 5.449335 -14.550665 39.101330 8.154796e-13



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5284_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19669_G|A,
19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T,
22131_G|C, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22332_G|T, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22813_G|T, 22858_C|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24700_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25081_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29284_C|T, 29383_G|A, 29466_C|T,
29510_A|C, 29734_29759

Case 46 (XFJ): OZ262381


Target: 24 samples Number of changes: 146
BC: JN.1.53 + XFJ.1 BC BR: 11-12 BC BR coord: 4839 - 4840
Direction L1: << Initial region span: 1-9,12-146Gap history (edge excluded): 9-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.13e-02
Rec. model vs L1: 1.29e-158Rec. model vs L2: 3.31e-16
Flags: Model_1BP_Best

JN.1.53 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.53 62 9 15.728510 NaN NaN NaN * * *
LF.7.9.3 20 5 11.825673 5.189982 25.620036 1.246501e-04 *
XFB.3 56 5 11.670112 4.885385 26.229230 9.188250e-05 *
XEL.5 19 5 11.593891 -15.870858 67.741715 8.901246e-14
LC.1 10 5 11.297148 -2.806209 41.612418 4.202505e-08
XEC.35.1 28 5 11.252812 -1.779095 39.558190 1.171278e-07
LF.7.1.11 20 5 11.163617 -8.501504 53.003008 1.413192e-10
XEC.4.7 13 5 11.141517 -1.741355 39.482709 1.219079e-07
KP.2.3 4440 9 11.116294 9.606882 16.786236 1.030630e-02 * *
XEC.23 142 5 11.050090 -1.999132 39.998263 9.399728e-08
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 12 309.884615 NaN NaN NaN * * *
XFJ.3 14 12 289.265270 283.628835 -263.257669 3.959117e-12 *
LF.7.9 20 7 259.623071 256.376545 -208.753090 5.766367e-24
LF.7.2.1 67 7 196.506412 193.350209 -82.700418 2.451842e-51
LF.7.9.3 20 29 191.091612 185.303736 -66.607472 7.863094e-55
PC.3 42 7 188.249405 185.108240 -66.216481 6.470026e-55
LF.7.9.1 48 29 185.630105 177.546997 -51.093994 3.353268e-58
PY.2 17 29 185.498143 177.436089 -50.872177 3.003972e-58
LF.7 58 7 183.108050 179.931167 -55.862333 3.641335e-57
PC.3.1 27 7 180.683815 177.542650 -51.085300 3.353268e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2308_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11812_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 46 (XFJ): OZ276211


Target: 24 samples Number of changes: 147
BC: LP.8.1 + XFJ.1 BC BR: 12-13 BC BR coord: 4839 - 4840
Direction L1: << Initial region span: 1-6,13-147Gap history (edge excluded): 6-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.83e-02
Rec. model vs L1: 2.11e-186Rec. model vs L2: 2.67e-06
Flags: Model_1BP_Best

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 6 12.349269 NaN NaN NaN * * *
LF.7.9.3 20 5 11.825673 -4.810018 53.620036 2.328374e-02 * *
XFB.3 56 5 11.670112 -5.114615 54.229230 1.716299e-02 * *
XEL.5 19 5 11.593891 -25.870858 95.741715 1.662689e-11 *
LC.1 10 5 11.297148 -12.806209 69.612418 7.849977e-06 *
XEC.35.1 28 5 11.252812 -11.779095 67.558190 2.187863e-05 * *
LF.7.1.11 20 5 11.163617 -18.501504 81.003008 2.639741e-08 *
XEC.4.7 13 5 11.141517 -11.741355 67.482709 2.277152e-05 * *
XEC.23 142 5 11.050090 -11.999132 67.998263 1.755802e-05 * *
LD.1.1 11 5 10.972996 -24.599596 93.199192 5.920590e-11 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 13 309.884615 NaN NaN NaN * * *
XFJ.3 14 13 289.265270 283.628835 -263.257669 3.959117e-12 *
LF.7.9 20 8 259.623071 256.376545 -208.753090 5.766367e-24
LF.7.2.1 67 8 196.506412 193.350209 -82.700418 2.451842e-51
LF.7.9.3 20 30 191.091612 185.303736 -66.607472 7.863094e-55
PC.3 42 8 188.249405 185.108240 -66.216481 6.470026e-55
LF.7.9.1 48 30 185.630105 177.546997 -51.093994 3.353268e-58
PY.2 17 30 185.498143 177.436089 -50.872177 3.003972e-58
LF.7 58 8 183.108050 179.931167 -55.862333 3.641335e-57
PC.3.1 27 8 180.683815 177.542650 -51.085300 3.353268e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1173_T|C, 2308_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11812_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 46 (XFJ): OZ276211


Target: 24 samples Number of changes: 147
BC: LP.8.1 + XFJ.1 BC BR: 12-13 BC BR coord: 4839 - 4840
Direction L1: << Initial region span: 1-6,13-147Gap history (edge excluded): 6-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.83e-02
Rec. model vs L1: 2.11e-186Rec. model vs L2: 2.67e-06
Flags: Model_1BP_Best

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 6 12.349269 NaN NaN NaN * * *
LF.7.9.3 20 5 11.825673 -4.810018 53.620036 2.328374e-02 * *
XFB.3 56 5 11.670112 -5.114615 54.229230 1.716299e-02 * *
XEL.5 19 5 11.593891 -25.870858 95.741715 1.662689e-11 *
LC.1 10 5 11.297148 -12.806209 69.612418 7.849977e-06 *
XEC.35.1 28 5 11.252812 -11.779095 67.558190 2.187863e-05 * *
LF.7.1.11 20 5 11.163617 -18.501504 81.003008 2.639741e-08 *
XEC.4.7 13 5 11.141517 -11.741355 67.482709 2.277152e-05 * *
XEC.23 142 5 11.050090 -11.999132 67.998263 1.755802e-05 * *
LD.1.1 11 5 10.972996 -24.599596 93.199192 5.920590e-11 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 13 309.884615 NaN NaN NaN * * *
XFJ.3 14 13 289.265270 283.628835 -263.257669 3.959117e-12 *
LF.7.9 20 8 259.623071 256.376545 -208.753090 5.766367e-24
LF.7.2.1 67 8 196.506412 193.350209 -82.700418 2.451842e-51
LF.7.9.3 20 30 191.091612 185.303736 -66.607472 7.863094e-55
PC.3 42 8 188.249405 185.108240 -66.216481 6.470026e-55
LF.7.9.1 48 30 185.630105 177.546997 -51.093994 3.353268e-58
PY.2 17 30 185.498143 177.436089 -50.872177 3.003972e-58
LF.7 58 8 183.108050 179.931167 -55.862333 3.641335e-57
PC.3.1 27 8 180.683815 177.542650 -51.085300 3.353268e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1173_T|C, 2308_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11812_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 46 (XFJ): OZ280587


Target: 24 samples Number of changes: 144
BC: JN.1.8.1 + XFJ.1 BC BR: 11-12 BC BR coord: 4839 - 4840
Direction L1: << Initial region span: 1-11,12-144Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 7.19e-05
Rec. model vs L1: 4.87e-121Rec. model vs L2: 3.58e-21
Flags: Model_1BP_Best

JN.1.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.8.1 1498 11 18.509376 NaN NaN NaN * * *
XDY.3 16 8 17.874592 10.021450 3.957100 2.055133e-04 *
MC.11.3 19 8 17.009594 9.156452 5.687095 8.653168e-05 *
MC.24.1 25 8 16.694335 8.841193 6.317613 6.314986e-05 *
KP.3.7 29 8 16.407356 8.554214 6.891573 4.748959e-05 *
LQ.1.2 32 8 16.325319 8.472177 7.055646 4.361977e-05 *
KP.2.11 40 8 16.161874 8.308732 7.382535 3.717032e-05 *
JN.1.50.1 48 8 16.040725 2.458124 19.083752 1.070468e-07
JN.10 47 8 16.037928 8.184786 7.630429 3.280269e-05 *
KP.2.1 47 8 15.952397 8.077749 7.844503 2.953307e-05 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 12 292.083200 NaN NaN NaN * * *
XFJ.3 14 12 285.078963 279.442528 -246.885056 3.239797e-06 *
LF.7.9 20 3 243.082377 238.009337 -164.018673 3.277373e-24
LF.7.2.1 67 3 181.001759 175.930259 -39.860518 3.585291e-51
PC.3 42 10 169.389947 167.243089 -22.486178 6.062851e-55
LF.7 58 3 167.259247 162.151348 -12.302696 3.714895e-57
LF.7.1 165 3 167.247168 146.263393 19.473214 4.690063e-64
PC.4 10 3 166.103443 160.925043 -9.850086 1.091279e-57
LF.7.9.3 20 3 164.047104 159.091847 -6.183695 1.741828e-58
PY.1 82 12 161.490050 161.490050 -10.980101 1.920048e-57 *



Target sequence

, 241_C|T, 519_524, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3876_C|T, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11893_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21610_.|ATGCCGCTGTTT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23063_A|T, 23075_T|C, 23156_A|G, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

Case 46 (XFJ): USA/CA-CDPH-6000021782/2025


Target: 24 samples Number of changes: 146
BC: LP.8.1 + XFJ.1 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,7-146Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.50e-192Rec. model vs L2: 1.55e-06
Flags: Model_2BP_Bad_L1_opp

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 4 7.743010 NaN NaN NaN * * *
MC.2 396 4 7.408891 7.408891 -4.817781 7.153381e-01 * *
NY.13 463 4 7.221759 7.221759 -4.443517 5.915554e-01 * *
KP.3 769 4 6.727092 6.727092 -3.454184 3.605949e-01 * *
XBB.1.32 20 3 6.598157 -3.401843 16.803687 1.444734e-05 * *
BA.5.2.44 120 3 5.006053 -4.993947 19.987895 2.931489e-06 *
BU.3 122 3 4.981293 -5.018707 20.037414 2.859110e-06 *
BT.2 227 3 4.355290 -5.644710 21.289419 1.530372e-06 *
BA.5.1.25 1675 3 4.146734 -5.853266 21.706533 1.240495e-06 *
BN.1.7 382 3 3.848124 -6.151876 22.303753 9.235878e-07 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 7 302.669687 NaN NaN NaN * * *
XFJ.3 14 7 290.757786 270.757786 -213.515571 6.722839e-06 *
LF.7.9 20 7 250.882577 230.882577 -133.765154 3.236386e-23 *
LF.7.2.1 67 7 189.402513 169.402513 -10.805027 6.451126e-50 *
PC.3 42 7 180.669337 151.943580 24.112839 1.685986e-57 *
LF.7 58 7 175.624961 155.624961 16.750078 6.684325e-56 *
PC.4 10 7 174.442640 154.442640 19.114720 2.053951e-56 *
PC.3.1 27 7 171.865144 143.153030 41.693940 2.566879e-61 *
LF.7.9.1 48 7 168.444888 139.395996 49.208009 5.976654e-63 *
PY.2 17 7 167.291545 130.504058 66.991884 8.233418e-67 *



Target sequence

, 241_C|T, 670_T|G, 709_G|T, 897_C|A, 1042_G|A, 1919_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20470_C|A, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|A, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27768_27772, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

Case 46 (XFJ): USA/CA-LACPHL-AY11911/2025


Target: 24 samples Number of changes: 149
BC: JN.1 + XFJ.1 BC BR: 29-30 BC BR coord: 12771 - 12772
Direction L1: << Initial region span: 1-29,30-149Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.97e-15
Rec. model vs L1: 5.60e-82Rec. model vs L2: 5.00e-29
Flags: Model_1BP_Best

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 29 36.851243 NaN NaN NaN * * *
JN.1.4 8971 29 33.928911 33.928911 -3.857822 5.393369e-02 * *
KP.3.1.1 12013 29 22.001203 16.667411 30.665177 1.713034e-09 *
MC.13 807 26 21.562333 10.652758 42.694485 4.203936e-12
JN.1.16.1 466 24 16.808532 4.776861 54.446278 1.174910e-14
JN.1.7 1974 24 15.175852 3.106624 57.786753 2.211733e-15
MC.19 221 24 13.940467 -3.367814 70.735628 3.409384e-18
KP.2 1589 24 12.301415 10.802039 42.395921 4.859916e-12
KP.3.3 1715 24 11.826561 11.386676 41.226649 8.723505e-12
KP.1.1.1 578 24 11.276705 -0.737140 65.474279 4.753811e-17
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 30 267.083694 NaN NaN NaN * * *
XFJ.3 14 6 246.814578 238.860040 -211.720079 5.521261e-13
LF.7.9 20 28 223.053004 218.611015 -171.222030 8.862882e-22
LF.7.2.1 67 28 160.026668 155.599717 -45.199433 3.825425e-49
JN.1.4 8971 4 159.058345 120.094623 25.810754 1.455640e-64
LF.7.9.3 20 28 158.329306 153.887317 -41.774634 6.884377e-50
LF.7.9.1 48 28 152.867799 148.425810 -30.851619 2.928308e-52
PY.2 17 28 152.735837 148.293848 -30.587696 2.571334e-52
PC.3 42 28 151.784699 147.342710 -28.685420 9.944403e-53
LF.7.1 165 28 148.980463 144.556823 -23.113646 6.107973e-54



Target sequence

, 222, 241_C|T, 670_T|G, 897_C|A, 1158_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7482_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10681_C|T, 11042_G|T, 11094_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|G, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25844_C|T, 25919_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29690_G|T, 29734_29759

Case 46 (XFJ): USA/MA-MASPHL-14074/2025


Target: 24 samples Number of changes: 150
BC: JN.1 + XFJ.1 BC BR: 5-6 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-5,7-150Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.72e-59 Rec. model vs L2: 1.13e-09
Flags: Model_2BP_Bad_L1_opp

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 5 2.994024 NaN NaN NaN * * *
BA.4 10442 4 1.503026 -12.358458 36.716916 2.144906e-07 *
BA.4.6 19369 4 0.776654 -13.122193 38.244386 1.003100e-07 *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 7 280.438942 NaN NaN NaN * * *
XFJ.3 14 7 275.318741 265.318741 -200.637483 5.976023e-03 * *
LF.7.9 20 7 245.718955 235.718955 -141.437910 8.342488e-16 *
PC.3 42 7 174.780514 156.054758 17.890485 2.104872e-50 *
LF.7.2.1 67 7 173.494668 163.494668 3.010665 3.584071e-47 *
LF.7.9.1 48 22 166.461577 143.507920 42.984160 7.498966e-56
LF.7 58 7 159.967518 149.967518 30.064964 4.792297e-53 *
PC.4 10 7 158.792875 148.792875 32.414250 1.479952e-53 *
LF.7.1 165 7 158.231093 148.231093 33.537813 8.411460e-54 *
PC.3.1 27 7 156.272177 137.560064 54.879872 1.954111e-58 *



Target sequence

, 241_C|T, 492_C|T, 580_T|C, 670_T|G, 897_C|A, 1851_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9907_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12253_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18129_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C,
22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A,
27807_C|T, 27810_T|C, 27970_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29734_29759

Case 46 (XFJ): IGS-10285-CVDP-2AAB5C9E-0709-4787-8906-A3F7486EE388


Target: 24 samples Number of changes: 148
BC: XFJ.1 + LF.7 + XFJ.1 BC BR: 9-10, 13-14 BC BR coord: 4330 - 4331, 7841 - 7842
Direction L1: << Initial region span: 1-9,11-13,14-148Gap history (edge excluded): 9-14 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.37e-04
Rec. model vs L1: 7.78e-16Rec. model vs L2: 1.36e-87
Flags: Model_2BP_Best

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 9 15.114291 None None None * * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 11 12.675918 NaN NaN NaN * * *
NL.4.1 26 12 9.730528 -10.269472 30.538945 2.388130e-06 *
JN.1.1.6 13 12 8.025780 -11.974220 33.948441 4.340961e-07 *
XEC.39 155 12 7.620273 -12.379727 34.759454 2.895320e-07 *
KS.1 505 11 7.545340 -2.454660 14.909319 5.916560e-03 * *
EA.1 124 13 6.980938 -23.019062 56.038124 6.931118e-12
HF.1.1 292 13 6.980938 -30.070499 70.140998 6.012114e-15
EA.2 17 13 6.980938 -23.019062 56.038124 6.931118e-12
BA.5.2.35 1368 13 6.978010 -23.021990 56.043981 6.931118e-12
BQ.1.1.52 476 13 6.968253 -23.031747 56.063494 6.862152e-12
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 14 290.448367 NaN NaN NaN * * *
XFJ.3 14 14 270.809714 285.918573 -257.837145 2.939577e-09 *
LF.7.9 20 1 229.837314 240.081891 -166.163783 3.632669e-29
LF.7 58 1 182.882400 180.206482 -46.412964 3.604489e-55
LF.7.2.1 67 1 168.121624 178.366201 -42.732402 5.724557e-56
PC.3 42 17 158.301525 169.861290 -25.722580 1.158957e-59
LF.7.1 165 17 156.766308 168.301276 -22.602553 2.435387e-60
LF.7.9.1 48 20 156.736585 162.886795 -11.773590 1.083586e-62
PY.2 17 20 155.305341 161.498110 -8.996219 2.712473e-63
PC.4 10 1 153.511694 163.756271 -13.512543 2.586423e-62



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4665_G|A, 5239_C|T, 6183_A|G, 7006_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15250_A|G, 15714_C|T, 15756_T|A, 16600_T|C,
16605_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28419_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29734_29759

Case 46 (XFJ): IGS-10285-CVDP-3BC3A18F-E0E3-415C-97ED-0C225785CACE


Target: 24 samples Number of changes: 146
BC: XFJ.1 + KP.2.5 + XFJ.1BC BR: 5-6, 11-12 BC BR coord: 3037 - 3038, 5238 - 5239
Direction L1: << Initial region span: 1-5,7-11,12-146Gap history (edge excluded): 5-12 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.32e-05
Rec. model vs L1: 8.95e-16Rec. model vs L2: 1.60e-202
Flags: Model_2BP_Best

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 5 5.748333 None None None * * *
|||||

KP.2.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.5 66 7 15.417185 NaN NaN NaN * * *
JN.1.2 650 7 13.151366 3.151366 7.697269 1.038300e-01 * *
AY.86 33 11 8.955276 -42.156247 98.312495 2.190844e-21
XBB.1.5.49 1290 9 5.238244 -24.761756 63.523513 7.855322e-14
BA.5.1.22 4997 9 4.571351 -20.370538 54.741077 6.334565e-12
BE.3 3742 9 4.169489 -25.830511 65.661022 2.694442e-14
AY.90 1220 11 3.841100 -41.691015 97.382029 3.487855e-21
B.1.241 765 11 3.614683 -36.560117 87.120234 5.895072e-19
BA.2.10 14971 9 3.478889 -26.521111 67.042222 1.351468e-14
BA.5.5 23560 9 3.428939 -9.117326 32.234652 4.894419e-07
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 12 308.218988 NaN NaN NaN * * *
XFJ.3 14 12 300.565137 306.365050 -304.730101 5.004514e-04 * *
LF.7.9 20 12 254.759708 260.559622 -213.119243 6.404765e-24 *
LF.7.2.1 67 12 193.045558 198.753608 -89.507217 9.224286e-51 *
PC.3 42 12 184.457844 190.233660 -72.467319 1.839686e-54 *
LF.7 58 12 179.573872 185.356394 -62.712788 1.397612e-56 *
PC.4 10 12 178.328728 184.128641 -60.257282 4.105593e-57 *
LF.7.9.1 48 12 177.480758 183.238111 -58.476223 1.685986e-57 *
LF.7.1 165 12 176.386507 182.155876 -56.311752 5.696975e-58 *
PY.2 17 12 176.070566 181.870479 -55.740959 4.284207e-58 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3053_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5219_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 25919_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29690_G|T, 29734_29759

Case 46 (XFJ): IGS-10285-CVDP-5C418B6D-4A8E-423C-9873-BB3B605DD9B9


Target: 24 samples Number of changes: 146
BC: XFJ.1 + GA.4.1 + XFJ.1BC BR: 138-139, 140-141 BC BR coord: 28361 - 28362, 28877 - 28878
Direction L1: >> Initial region span: 1-138,139-140,141-146Gap history (edge excluded): 138-141 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.30e-01
Rec. model vs L1: 1.15e-17Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 138 307.554472 NaN NaN NaN * * *
XFJ.3 14 138 302.378606 310.037560 -300.075121 6.313911e-03 * *
LF.7.9 20 138 262.340879 269.837314 -219.674628 2.185188e-20 *
LF.7.2.1 67 138 210.988783 218.413337 -116.826673 1.018747e-42 *
LF.7 58 138 197.572545 205.122300 -90.244600 1.714437e-48 *
PC.3 42 146 192.777543 190.890956 -61.781913 1.132690e-54
LF.7.1 165 146 189.604172 189.067843 -58.135686 1.835249e-55
PC.4 10 138 185.958101 193.511694 -67.023388 1.555831e-53 *
PC.3.1 27 138 183.581089 191.163082 -62.326164 1.491221e-54 *
JN.1.4 8971 146 179.139713 178.456944 -36.913889 4.504629e-60
|||||

GA.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
GA.4.1 97 140 9.361926 NaN NaN NaN * * *
B.1.1.528 51 140 9.361926 9.361926 -14.723851 1.000000 * *
B.1.1.322 31 140 9.361926 9.361926 -14.723851 1.000000 * *
C.37.1 77 140 9.268469 9.268469 -14.536938 0.913931 * *
MC.1.4.1 41 140 9.156617 9.156617 -14.313235 0.814647 * *
B.1.1.408 15 140 9.075724 9.075724 -14.151448 0.752014 * *
XBB.3.1 13 140 8.390910 8.390910 -12.781820 0.379083 * *
XBB.1.43.1 22 140 7.975631 7.975631 -11.951262 0.250324 * *
FY.8.1 29 140 7.232504 7.232504 -10.465008 0.119433 * *
FY.4.1 61 140 7.229223 7.229223 -10.458446 0.118837 * *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 141 7.551709 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G,
18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22093_G|C, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T,
28362_28370, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 46 (XFJ): IGS-10285-CVDP-945917A7-03F4-44B7-B15E-9DAC718B9032


Target: 24 samples Number of changes: 146
BC: XFJ.1 + GA.4.1 + XFJ.1BC BR: 138-139, 140-141 BC BR coord: 28361 - 28362, 28877 - 28878
Direction L1: >> Initial region span: 1-138,139-140,141-146Gap history (edge excluded): 138-141 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.30e-01
Rec. model vs L1: 1.15e-17Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFJ.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 138 307.554472 NaN NaN NaN * * *
XFJ.3 14 138 302.378606 310.037560 -294.075121 6.313911e-03 * *
LF.7.9 20 138 262.340879 269.837314 -213.674628 2.185188e-20 *
LF.7.2.1 67 138 200.697070 208.121624 -90.243247 3.443538e-47 *
PC.3 42 146 192.777543 190.890956 -55.781913 1.132690e-54
LF.7 58 138 187.136582 194.686337 -63.372674 5.038004e-53 *
PC.4 10 138 185.958101 193.511694 -61.023388 1.555831e-53 *
PC.3.1 27 138 183.581089 191.163082 -56.326164 1.491221e-54 *
LF.7.1 165 146 179.520565 178.984236 -31.968471 7.653060e-60
LF.7.9.1 48 138 170.950858 178.501748 -31.003495 4.711968e-60 *
|||||

GA.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
GA.4.1 97 140 9.361926 NaN NaN NaN * * *
B.1.1.528 51 140 9.361926 9.361926 -14.723851 1.000000 * *
B.1.1.322 31 140 9.361926 9.361926 -14.723851 1.000000 * *
C.37.1 77 140 9.268469 9.268469 -14.536938 0.913931 * *
MC.1.4.1 41 140 9.156617 9.156617 -14.313235 0.814647 * *
B.1.1.408 15 140 9.075724 9.075724 -14.151448 0.752014 * *
XBB.3.1 13 140 8.390910 8.390910 -12.781820 0.379083 * *
XBB.1.43.1 22 140 7.975631 7.975631 -11.951262 0.250324 * *
FY.8.1 29 140 7.232504 7.232504 -10.465008 0.119433 * *
FY.4.1 61 140 7.229223 7.229223 -10.458446 0.118837 * *
|||||

XFJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFJ.1 59 141 7.551709 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18894_C|T, 19955_C|T, 20055_A|G, 20799_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22093_G|C, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23728_T|C, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25844_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C,
28311_C|T, 28362_28370, 28877_A|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 52 (XES): USA/IVY-G25Y93M8/2025


Target: 59 samples Number of changes: 152
BC: KP.3.3 + KP.2.3.15 + KP.3.3BC BR: 11-12, 16-17 BC BR coord: 4330 - 4331, 6470 - 6471
Direction L1: << Initial region span: 1-11,12-16,17-152Gap history (edge excluded): 11-17 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.08e-10
Rec. model vs L1: 9.36e-20 Rec. model vs L2: 4.00e-70
Flags: Model_2BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 11 5.816434 None None None * * *
|||||

KP.2.3.15 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.15 59 16 13.298012 NaN NaN NaN * * *
AY.70 861 12 5.662483 -41.890318 109.780635 1.074701e-24
FL.24 72 12 4.611686 -39.810180 105.620360 8.602409e-24
BF.7 11554 14 4.040111 -5.197174 36.394348 9.283753e-09
AA.5 52 12 3.797674 -47.083547 120.167094 5.958373e-27
AY.85 549 12 3.743404 -37.364394 100.728788 9.919050e-23
AY.127 7489 12 3.663016 -27.742787 81.485573 1.494111e-18
BA.2.52 379 13 3.469920 -26.530080 79.060159 5.035595e-18
NY.16.1 20 12 3.366891 -34.734554 95.469109 1.376146e-21
HY.1 179 13 3.221021 -26.778979 79.557958 3.921725e-18
|||||

KP.3.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 17 208.255914 NaN NaN NaN * * *
KP.3.1 1957 15 190.995817 178.431488 -20.862975 3.324640e-16
KP.3.1.1 12013 17 186.671839 192.864437 -49.728875 6.177113e-10 *
KP.2.3 4440 17 178.490339 173.622995 -11.245989 2.722449e-18 *
KP.3 769 17 157.248598 152.328392 31.343217 1.536946e-27 *
MC.24.1 25 17 155.723534 150.865679 34.268643 3.551545e-28 *
XEC.2 921 57 153.328110 147.582506 40.834988 1.336384e-29
MC.8.1 174 48 152.771335 125.120295 85.759410 2.341563e-39
PG.3 31 48 152.651791 122.567783 90.864434 1.828331e-40
KP.2 1589 17 150.262194 145.352550 45.294900 1.436993e-30 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1358_G|A, 1404_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4891_C|T, 5310_C|T, 6022_A|T, 6183_A|G, 6471_C|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8836_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 17745_C|T, 18163_A|G, 18492_A|G, 18642_A|C, 18894_C|T, 19011_C|T, 19803_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22000_C|A, 22032_T|C, 22033_C|A, 22034_A|G, 22054_T|C, 22194_22196, 22200_T|G, 22208_C|T,
22225_G|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23126_G|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27373, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/AR-CDC-2-8381796/2025


Target: 269 samples Number of changes: 142
BC: KP.2 + KP.3.1.1 + KP.2BC BR: 10-11, 20-21 BC BR coord: 6183 - 6184, 9533 - 9534
Direction L1: << Initial region span: 1-10,13-20,21-142Gap history (edge excluded): 10-21 -> 10-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.83e-04
Rec. model vs L1: 7.15e-28Rec. model vs L2: 9.68e-29
Flags: Model_2BP_Best

KP.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 10 18.699517 None None None * * *
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 13 12.244538 NaN NaN NaN * * *
JN.1 17255 12 11.352938 11.157600 1.684800 2.351374e+00 * *
JN.1.1 3081 13 10.526826 0.496192 23.007616 5.489985e-05 * *
NL.15 13 17 10.497880 -22.343583 68.687166 6.611274e-15
KP.2.8 51 17 9.131004 -28.097270 80.194541 2.104224e-17
XBB.1.5.20 860 18 8.615822 -61.384178 146.768357 7.335481e-32
BR.5 15 18 8.615822 -70.278195 164.556391 1.005493e-35
BR.4 11 18 8.615822 -70.278195 164.556391 1.005493e-35
BR.1.2 119 18 8.615822 -70.278195 164.556391 1.005493e-35
BR.2.1 313 18 8.606222 -61.393778 146.787557 7.262492e-32
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 21 216.533120 NaN NaN NaN * * *
KP.3.1.1 12013 1 210.962964 200.660225 -111.320449 9.644246e-16
JN.1 17255 1 202.008374 190.850774 -91.701548 5.294676e-20
XEC.2 921 17 197.785733 212.810206 -135.620411 1.823670e-10
MC.24.1 25 39 196.620020 213.609804 -137.219608 4.058652e-10
KS.1.1.2 252 1 195.583419 205.072607 -120.145215 7.974040e-14
KP.3 769 17 188.912328 203.749124 -117.498247 2.119524e-14
XEK.5 28 21 186.525203 205.243853 -120.487706 9.451669e-14 *
XEC.9 305 17 186.478244 200.410249 -110.820498 7.510946e-16
XEK.1 88 21 185.726148 204.507477 -119.014953 4.509523e-14 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 6989_T|C, 7842_A|G, 7936_G|A, 8293_C|T, 8386_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9532_C|T, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22546_A|G, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25163_C|A, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/CA-CDPH-500146881/2025


Target: 269 samples Number of changes: 135
BC: KP.2 + LF.7.1.4 + KP.2BC BR: 8-9, 10-11 BC BR coord: 6183 - 6184, 7118 - 7119
Direction L1: << Initial region span: 1-8,9-10,12-135Gap history (edge excluded): 8-12 -> 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.34e-08
Rec. model vs L1: 2.65e-19Rec. model vs L2: 6.49e-120
Flags: Model_2BP_Best

KP.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 8 9.339591 None None None * * *
|||||

LF.7.1.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.1.4 12 10 9.812013 NaN NaN NaN * * *
BF.7.19 413 11 7.315788 2.329466 -0.658931 5.642574e-04 * *
BA.5.1.31 43 9 5.680838 -4.319162 12.638323 7.301616e-07 *
XFH.2 15 9 5.680838 -4.319162 12.638323 7.301616e-07 *
XFH.1 10 9 5.680838 -4.319162 12.638323 7.301616e-07 *
LF.7.1.8 44 9 5.680838 -4.319162 12.638323 7.301616e-07 *
LF.7.1.5 40 9 5.680838 -4.319162 12.638323 7.301616e-07 *
LF.7.1.6 14 9 5.680838 -4.319162 12.638323 7.301616e-07 *
LF.7.1.10 13 9 5.680838 -4.319162 12.638323 7.301616e-07 *
PL.1.1 12 9 5.680838 -4.319162 12.638323 7.301616e-07 *
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 12 227.030213 NaN NaN NaN * * *
MC.24.1 25 36 207.337064 206.174727 -114.349455 8.361236e-13
KS.1.1.2 252 2 198.574836 197.301174 -96.602348 1.169249e-16
XEC.2 921 2 197.286315 201.783492 -105.566985 1.036854e-14
XEC.39 155 2 195.810694 199.541295 -101.082591 1.098314e-15
XEC.9 305 12 193.268152 192.615335 -87.230669 1.079536e-18 *
XEC.8 592 2 193.033005 198.159555 -98.319110 2.763123e-16
KP.3.3 1715 12 192.457197 200.050794 -102.101587 1.829013e-15 *
XEC.32 42 12 192.170275 191.534526 -85.069051 3.666057e-19 *
XEK.5 28 12 191.854108 191.292466 -84.584933 2.869440e-19 *



Target sequence

, 241_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6310_C|T, 6701_C|T, 7528_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13551_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

Case 55 (XEQ): USA/CO-CDC-QDX33808363/2025


Target: 269 samples Number of changes: 146
BC: JN.1 + KP.2 BC BR: 20-21 BC BR coord: 8866 - 8867
Direction L1: << Initial region span: 1-19,21-146Gap history (edge excluded): 19-21
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.08e-15
Rec. model vs L1: 1.10e-21Rec. model vs L2: 3.08e-35
Flags: Model_1BP_Best

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 19 27.756261 NaN NaN NaN * * *
KP.2.2 1334 19 18.419532 8.419532 41.160937 4.088859e-09 *
KP.2.3.10 10 9 17.811654 -33.065210 124.130421 3.934554e-27
PL.1.1 12 9 17.542321 -53.203181 164.406362 7.050252e-36
KP.3.1.2 28 9 16.671559 -2.016098 62.032197 1.201543e-13
JN.1.69 32 9 16.648503 -29.630829 117.261658 1.220948e-25
LF.7.2 35 9 16.500916 -48.563748 155.127496 7.300137e-34
JN.1.50.2 33 9 16.493668 -38.546208 135.092416 1.640445e-29
MK.1 151 9 16.148381 -34.517762 127.035525 9.183263e-28
KP.2.3.7 54 9 16.068823 -44.009436 146.018872 6.942924e-32
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 21 207.686381 NaN NaN NaN * * *
MC.24.1 25 46 204.783064 177.052837 -86.105674 4.983793e-14
JN.1 17255 1 193.685648 165.951070 -63.902140 7.494105e-19
MR.2 14 46 189.417525 157.189625 -46.379249 1.175710e-22
XEC.2 921 21 187.695236 187.695236 -107.390471 2.081869e-09 *
XEK.5 28 47 186.826807 162.280931 -56.561861 1.909234e-20
XEC.2.2 273 47 185.619187 173.039121 -78.078242 8.992236e-16
XEK.1 88 47 185.381124 161.504865 -55.009729 8.795911e-21
XEC.9 305 47 184.400272 163.854822 -59.709645 9.223014e-20
XEC.2.1 265 47 184.093029 145.075317 -22.150634 6.439060e-28



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4228_A|T, 4321_C|T, 4901_C|T, 6183_A|G, 6312_C|T, 6651_C|T, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
8861_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12439_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14396_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18329_C|A, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22149_A|G, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/CT-DPH-1286600001/2025


Target: 269 samples Number of changes: 138
BC: KS.1.1.2 + MC.24.1 BC BR: 40-41 BC BR coord: 17411 - 17412
Direction L1: << Initial region span: 1-34,43-138Gap history (edge excluded): 34-43
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.49e-16
Rec. model vs L1: 4.77e-36Rec. model vs L2: 1.53e-36
Flags: Model_1BP_Best

KS.1.1.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1.1.2 252 34 47.019733 NaN NaN NaN * * *
KP.3.1.1 12013 27 40.138102 17.412739 65.174522 5.031312e-08
XEC.2 921 24 33.034695 13.813580 72.372840 1.374742e-09
JN.1.13.1 751 27 32.561232 9.482411 81.035178 1.801169e-11
LB.1.3 778 27 32.215153 8.764540 82.470921 8.811178e-12
JN.1 17255 34 31.655936 25.492705 49.014590 1.624728e-04 * *
JN.1.7 1974 18 30.637924 -1.798158 103.596317 2.273593e-16
JN.1.32 436 18 30.396258 -1.226359 102.452717 4.040472e-16
MC.1.1 107 18 30.184200 -45.383964 190.767928 2.679093e-35
JN.1.8.3 121 27 29.995699 -15.208419 130.416839 3.410545e-22
|||||

MC.24.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.24.1 25 43 181.001520 NaN NaN NaN * * *
MC.1 932 49 172.187927 146.537821 -65.075642 1.108975e-11
KP.3.3 1715 43 169.068034 159.832038 -91.664076 6.556852e-06 *
JN.1.4 8971 4 167.852413 142.858196 -57.716391 2.797164e-13
MC.19 221 51 165.658470 133.634976 -39.269952 2.756458e-17
KP.2 1589 43 165.101600 155.866187 -83.732375 1.243706e-07 *
KS.1.1.2 252 2 164.872022 130.085858 -32.171717 7.917827e-19
MC.11 393 49 164.114415 131.015160 -34.030320 2.006780e-18
KP.3 769 49 163.561223 148.132525 -68.265051 5.465393e-11
MC.13 807 49 163.135411 137.454608 -46.909216 1.257061e-15



Target sequence

, 203_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 9814_T|C,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11124_C|T, 11288_11296, 11727_G|A, 12076_C|T, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14773_G|A, 15714_C|T,
15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18375_T|C, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C,
22684_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29734_29759

Case 55 (XEQ): USA/DC-CDC-2-8398675/2025


Target: 269 samples Number of changes: 145
BC: LB.1.3.2 + KP.2 BC BR: 13-14 BC BR coord: 7118 - 7119
Direction L1: << Initial region span: 1-10,16-145Gap history (edge excluded): 10-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.01e-07
Rec. model vs L1: 4.68e-67Rec. model vs L2: 1.32e-16
Flags: Model_1BP_Best

LB.1.3.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LB.1.3.2 390 10 20.309495 NaN NaN NaN * * *
MC.28 304 10 19.754430 -1.019295 42.038590 5.644495e-08 *
JN.1 17255 12 18.739122 18.543784 2.912431 1.772542e+01 *
LB.1.3 778 10 17.872098 11.441243 17.117514 1.455239e-02 * *
JN.1.32 436 10 17.755495 11.901429 16.197143 2.305206e-02 * *
LB.1.7 1971 10 16.294931 3.115380 33.769240 3.527222e-06 *
JN.1.8.3 121 10 14.129862 -2.260347 44.520694 1.633428e-08 *
JN.1.16.3 52 12 13.746642 3.746642 32.506716 6.622749e-06
NY.16 136 10 12.300606 -20.180270 80.360540 2.694901e-16 *
JN.1.4.2 736 10 12.145639 -4.247291 48.494581 2.244013e-09 *
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 16 201.442275 NaN NaN NaN * * *
KP.3.1.1 12013 3 193.114559 177.728291 -61.456583 2.447752e-02 *
KS.1.1.2 252 16 187.607156 167.607156 -41.214312 9.806992e-07 *
MC.24.1 25 41 186.620020 156.093432 -18.186865 9.835725e-12
KP.3.1 1957 41 184.031878 173.813810 -53.627620 4.880952e-04 *
MC.1 932 46 183.160501 135.289174 23.421652 9.063786e-21
JN.1 17255 1 183.114049 164.570265 -35.140530 4.714679e-08
XEC.2.1 265 41 177.565336 137.332696 19.334608 7.005544e-20
KP.3 769 49 177.548733 144.148001 5.703998 6.384969e-17
XEC.2 921 41 176.312932 155.380305 -16.760610 4.811559e-12



Target sequence

, 241_C|T, 504_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5704_G|T, 6183_A|G, 6701_C|T, 7279_C|T, 7294_G|A, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14676_C|T, 15714_C|T,
15756_T|A, 16392_T|C, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20389_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22323_C|T,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23185_C|T, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/IL-RIPHL_15496_G/2025


Target: 269 samples Number of changes: 147
BC: MC.24.1 + LB.1.7 + MC.24.1BC BR: 3-4, 43-44 BC BR coord: 896 - 897, 17409 - 17410
Direction L1: << Initial region span: 1-3,17-43,44-147Gap history (edge excluded): 3-44 -> 3-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.13e-28
Rec. model vs L1: 5.52e-38 Rec. model vs L2: 2.52e-54
Flags: Model_2BP_Best

MC.24.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.24.1 25 3 4.677997 None None None * * *
|||||

LB.1.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LB.1.7 1971 17 18.791066 NaN NaN NaN * * *
JN.1 17255 17 15.216481 -5.280363 122.560725 1.144537e+00 * *
JN.1.4 8971 17 15.116107 -4.483100 120.966201 2.534509e+00 * *
KP.2.3 4440 17 10.639991 -11.903808 135.807617 1.518549e-03 * *
JN.1.1 3081 33 10.526857 -19.939366 151.878733 4.918953e-07
BA.2.86.1 1343 17 7.355318 -18.370930 148.741861 2.364368e-06 *
JN.1.4.5 1757 39 6.345757 -36.794167 185.588335 2.354177e-14
LF.7.6 15 43 5.231571 -94.244932 300.489864 2.640105e-39
JN.1.7.1 120 43 4.761567 -50.407740 212.815479 2.876867e-20
B.1.1.318 1569 43 4.724562 -302.580461 717.160922 8.767591e-130
|||||

MC.24.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.24.1 25 44 184.698786 NaN NaN NaN * * *
KP.2 1589 30 181.969180 184.331518 -134.663037 6.441460e-03 *
MR.2 14 44 169.333247 174.052066 -114.104132 2.210228e-07 *
XEC.2 921 44 167.776614 172.458172 -110.916344 4.507221e-08 *
XEC.2.1 265 44 167.475708 172.148486 -110.296971 3.305807e-08 *
KP.3.1 1957 44 167.271401 171.952565 -109.905131 2.720133e-08 *
MC.8.1 174 59 166.171095 143.363447 -52.726894 1.042584e-20
XEK.5 28 44 165.161097 169.805808 -105.611616 3.168524e-09 *
XEC.2.2 273 44 163.953477 168.635326 -103.270653 9.834051e-10 *
XEK.1 88 44 163.715414 168.422805 -102.845610 7.971327e-10 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1738_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3787_C|T, 4184_G|A, 4321_C|T, 5300_G|A, 6183_A|G, 6701_C|T, 7331_G|T, 7393_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11109_C|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12827_T|C, 12880_C|T,
13339_T|C, 14265_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22048_T|C, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28396_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/IL-RIPHL_33562_G/2025


Target: 269 samples Number of changes: 145
BC: XEC.2 + KP.3 BC BR: 136-137 BC BR coord: 28271 - 28272
Direction L1: >> Initial region span: 1-136,137-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.73e-02
Rec. model vs L1: 8.12e-19Rec. model vs L2: 1.35e-28
Flags: Model_1BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 136 193.710444 NaN NaN NaN * * *
KP.3.1.1 12013 145 189.538884 180.134825 -46.269650 1.271898e-06
KP.2.3 4440 145 187.470520 177.966295 -41.932590 1.452223e-07
JN.1 17255 145 180.465957 171.209609 -28.419219 1.691898e-10
KS.1.1.2 252 111 178.369348 159.505838 -5.011677 1.396231e-15
JN.1.4 8971 145 173.726166 163.385510 -12.771021 6.761139e-14
KP.3.1 1957 145 169.602308 159.056996 -4.113991 8.902761e-16
KP.2 1589 138 159.016689 157.582056 -1.164113 2.036762e-16
KP.3.3 1715 136 153.170217 153.170217 7.659565 2.475721e-18 *
XEC.39 155 110 152.000195 149.885928 14.228144 9.269244e-20
|||||

KP.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3 769 137 15.147852 NaN NaN NaN * * *
JN.1.42.1 18 137 13.781451 13.781451 -9.562902 0.254107 * *
JN.1.51.1 24 137 13.685660 13.685660 -9.371320 0.231078 * *
JN.1.56 21 137 13.477848 13.477848 -8.955696 0.188247 * *
MC.36 49 137 13.000573 13.000573 -8.001146 0.116484 * *
JN.1.27 62 137 12.605402 12.605402 -7.210805 0.078473 * *
KP.3.4 62 137 12.511552 12.511552 -7.023105 0.071361 * *
MC.24 831 137 12.244533 12.244533 -6.489066 0.054749 * *
JN.1.52 150 137 11.735295 11.735295 -5.470591 0.032876 * *
LB.1.2.2 175 137 11.712458 11.712458 -5.424915 0.032065 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2761_A|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 6183_A|G, 6701_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14262_C|T, 14408_C|T, 15714_C|T,
15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18804_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22051_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24381_C|T, 24424_A|T, 24469_T|A, 24745_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26753_C|T, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28705_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/MN-MDH-46610/2025


Target: 269 samples Number of changes: 146
BC: KP.2 + CK.1 BC BR: 142-143 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-142,143-146Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.43e-14 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 142 200.779066 NaN NaN NaN * * *
KP.2.3 4440 146 195.425509 190.516695 -59.033391 3.483110e-05 *
XEC.2 921 136 189.789308 186.155651 -50.311302 4.450853e-07
JN.1 17255 145 180.547259 178.709717 -35.419435 2.600883e-10
JN.1.4 8971 146 177.946561 175.354170 -28.708340 9.079518e-12
KP.3.1.1 12013 145 177.786690 175.585106 -29.170211 1.142748e-11
KP.3.1 1957 145 168.299378 167.601554 -13.203108 3.891429e-15
KS.1.1.2 252 112 166.982337 160.603613 0.792774 3.566311e-18
KP.3 769 142 158.828011 158.828011 4.343977 6.044307e-19 *
KP.3.3 1715 136 156.894467 153.275910 15.448180 2.337979e-21
|||||

CK.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
CK.1 451 143 9.547834 NaN NaN NaN * * *
CB.1 82 144 9.064721 -0.935279 11.870559 2.795261e-05 * *
BA.2.60 31 144 8.948762 -1.051238 12.102477 2.491601e-05 * *
JN.1.38 247 143 8.096348 8.096348 -6.192696 2.334004e-01 * *
GR.1 120 144 7.582377 -7.750882 25.501764 3.066941e-08 *
XBB.1.5.80 186 144 7.120634 -2.879366 15.758731 3.996866e-06 *
BQ.1.12 2465 144 6.677357 5.622896 -1.245792 1.974214e-02 * *
KP.2.3 4440 144 5.298974 4.908814 0.182373 9.657698e-03 * *
BF.4 1166 144 5.223763 -4.776237 19.552475 6.008022e-07 *
BA.5.3.2 887 144 5.073932 4.348427 1.303147 5.516564e-03 * *



Target sequence

, 241_C|T, 664_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 6864_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T,
17410_C|T, 18163_A|G, 18210_G|T, 18492_A|G, 18648_T|C, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22088_C|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25047_C|T, 25163_C|A, 25207_C|T, 25507_G|A,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29734_29759, 29807_T|A

Case 55 (XEQ): USA/NMDOH-2025009737/2025


Target: 269 samples Number of changes: 143
BC: JN.1 + MC.24.1 BC BR: 40-41 BC BR coord: 16949 - 16950
Direction L1: << Initial region span: 1-28,41-143Gap history (edge excluded): 28-41
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.38e-11
Rec. model vs L1: 5.29e-29Rec. model vs L2: 4.13e-44
Flags: Model_1BP_Best

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 28 37.933316 NaN NaN NaN * * *
KP.2.3 4440 28 35.954419 29.166822 37.666355 2.773195e+00 * *
KP.3.1.1 12013 28 32.660241 12.226126 71.547749 1.219079e-07 *
JN.1.4 8971 28 31.196677 24.752323 46.495353 3.354055e-02 * *
JN.1.48 10 11 24.419246 -26.330485 148.660969 2.196889e-24
MC.13.1 123 12 23.122272 -32.208864 160.417728 6.139833e-27
KP.2.3.11 56 11 22.642094 -43.657710 183.315419 6.538599e-32
JN.1.63 60 11 22.541687 -22.071041 140.142081 1.555617e-22
JN.1.2 650 28 22.494418 -2.361175 100.722350 5.647378e-14 *
JN.1.7 1974 28 22.121485 4.418752 87.162496 4.970080e-11 *
|||||

MC.24.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.24.1 25 41 206.620020 NaN NaN NaN * * *
KP.2 1589 19 204.474330 180.618363 -137.236726 5.109089e-12
MR.2 14 41 191.254480 186.756808 -149.513615 2.359066e-09 *
XEC.2 921 31 189.460717 184.793250 -145.586500 3.322943e-10
XEK.5 28 41 187.082331 187.082331 -150.164662 3.265020e-09 *
KP.3.1 1957 41 186.650574 182.163690 -140.327380 2.395126e-11 *
XEC.2.2 273 41 185.874711 185.874711 -147.749421 9.785003e-10 *
XEK.1 88 41 185.636648 185.636648 -147.273297 7.697156e-10 *
XEC.9 305 41 184.655796 184.655796 -145.311592 2.888828e-10 *
KP.2.3 4440 1 184.545901 155.379078 -86.758157 5.581498e-23



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1601_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6285_C|T, 6701_C|T, 7564_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 8947_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12685_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15720_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24090_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/NMDOH-2025013200/2025


Target: 269 samples Number of changes: 139
BC: JN.9 + KP.2 BC BR: 11-12 BC BR coord: 7118 - 7119
Direction L1: << Initial region span: 1-11,12-139Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.90e-02
Rec. model vs L1: 5.28e-125Rec. model vs L2: 2.54e-32
Flags: Model_1BP_Best

JN.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.9 55 11 20.431130 NaN NaN NaN * * *
JN.11 67 10 15.851612 5.851612 22.296776 4.655716e-07 *
JN.18 316 11 15.144993 15.144993 3.710015 5.067032e-03 * *
JN.3 321 10 14.930933 -1.375664 36.751328 3.390071e-10 *
BA.2.86.1 1343 10 14.446675 4.446675 25.106651 1.142359e-07 *
MC.10.2.1 11 10 13.901608 -10.526839 55.053679 3.600927e-14 *
KP.2.3.13 25 10 13.869085 -0.517726 35.035452 7.971327e-10 *
JN.7 82 9 13.649232 -5.489980 44.979961 5.534610e-12
NL.19 18 10 13.447284 3.447284 27.105433 4.202505e-08 *
JN.1.7 1974 11 13.362795 13.362795 7.274410 8.544949e-04 * *
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 12 221.528527 NaN NaN NaN * * *
XEC.2 921 1 198.733225 194.559029 -99.118058 1.936769e-12
KS.1.1.2 252 5 192.161982 178.803010 -67.606019 2.784635e-19
KP.3.3 1715 12 192.053222 192.053222 -94.106443 1.581868e-13 *
XEC.9 305 14 191.094001 184.696944 -79.393888 1.006382e-16
XEC.8 592 5 187.116748 180.098728 -70.197457 1.016669e-18
XEC.32 42 5 181.881976 172.252609 -54.505217 3.982350e-22
MC.24.1 25 14 181.358888 174.961831 -59.923662 5.955332e-21
KP.3.1.1 12013 1 180.974185 174.257093 -58.514186 2.942581e-21
KP.3 769 14 178.792602 172.394244 -54.788488 4.580793e-22



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 7945_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25003_A|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29700_A|G, 29734_29759

Case 55 (XEQ): USA/NMDOH-2025014470/2025


Target: 269 samples Number of changes: 142
BC: JN.9 + KP.2 BC BR: 12-13 BC BR coord: 7118 - 7119
Direction L1: << Initial region span: 1-12,13-142Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.54e-03
Rec. model vs L1: 1.32e-124Rec. model vs L2: 1.32e-33
Flags: Model_1BP_Best

JN.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.9 55 12 21.906785 NaN NaN NaN * * *
JN.11 67 11 18.228521 8.228521 17.542959 1.150861e-06 *
NL.19 18 11 17.426195 7.426195 19.147610 5.145362e-07 *
JN.18 316 12 16.818149 16.818149 0.363701 6.188887e-03 * *
JN.3 321 11 15.047946 -1.258651 36.517302 8.700983e-11 *
BA.2.86.1 1343 11 14.806444 4.806444 24.387112 3.745971e-08 *
LB.1.3.1 292 11 14.425151 4.425151 25.149698 2.561725e-08 *
JN.7 82 10 14.032355 -5.106858 44.213716 1.860827e-12
JN.1.7 1974 12 13.049726 13.049726 7.900548 1.426666e-04 * *
MC.24 831 12 12.672824 8.286013 17.427974 1.215932e-06 *
|||||

KP.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 13 201.681620 NaN NaN NaN * * *
KP.3.1.1 12013 3 190.932653 184.219710 -74.439421 2.613475e-08
JN.1 17255 1 181.936012 171.807102 -49.614203 1.060358e-13
KP.2.3 4440 3 174.405635 168.623435 -43.246870 4.409567e-15
MC.24.1 25 41 173.651463 154.961831 -15.923662 5.125802e-21
JN.1.4 8971 4 170.381607 164.594122 -35.188244 7.837709e-17
XEC.2 921 1 170.178188 165.842387 -37.684774 2.721985e-16
XEC.2.2 273 42 169.780712 153.296698 -12.593396 9.697538e-22
XEC.9 305 42 168.325918 156.821064 -19.642127 3.292680e-20
XEK.1 88 42 164.814103 149.955450 -5.910899 3.436512e-23



Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7842_A|G, 7945_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10125_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
16943_G|T, 17410_C|T, 18163_A|G, 18167_C|T, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24292_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27527_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28603_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 55 (XEQ): USA/NY-USAFSAM-S23702/2025


Target: 269 samples Number of changes: 144
BC: KP.2 + JN.1.52 BC BR: 136-137 BC BR coord: 28361 - 28362
Direction L1: >> Initial region span: 1-136,138-144Gap history (edge excluded): 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.01e-07 Rec. model vs L2: 5.24e-64
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 136 204.827501 NaN NaN NaN * * *
XEC.2 921 134 190.823447 186.492555 -60.985111 1.089458e-08
KS.1.1.2 252 136 185.749577 185.749577 -59.499153 5.172033e-09 *
XEC.8 592 134 181.561572 177.242591 -42.485182 1.047097e-12
KP.2.3 4440 144 177.462439 169.659460 -27.318919 5.319405e-16
XEC.18 165 134 172.919344 168.613832 -25.227664 1.870791e-16
KP.3.3 1715 134 172.642419 168.324704 -24.649408 1.399845e-16
KP.3.1.1 12013 136 169.006037 169.006037 -26.012074 2.763123e-16 *
JN.1 17255 141 167.703313 163.908312 -15.816624 1.693050e-18
XEC.39 155 134 167.689853 163.383549 -14.767098 1.001533e-18
|||||

JN.1.52 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.52 150 138 12.208037 NaN NaN NaN * * *
JN.1.4.3 129 138 11.562933 1.562933 16.874135 5.246625e-01 * *
MC.10.1 650 138 10.021102 -7.652555 35.305110 5.196189e-05 * *
MC.13 807 138 9.910126 -0.089874 20.179749 1.002588e-01 * *
KP.3.1 1957 138 8.940001 -1.059999 22.119999 3.800643e-02 * *
KP.2.3 4440 138 8.828691 7.802979 4.394041 2.690777e+02 * *
KP.3.1.1 12013 138 7.885735 -2.114265 24.228530 1.323355e-02 * *
JN.1.4 8971 138 7.454435 5.032233 9.935534 1.677685e+01 * *
BQ.1.1.1 1179 142 7.119877 -14.746907 49.493813 4.330490e-08
BN.1.3 1498 142 6.425820 -11.991691 43.983383 6.807981e-07



Target sequence

, 241_C|T, 509_523, 575_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6701_C|T, 7528_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9655_T|C, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12418_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15720_C|T, 15756_T|A, 16887_C|T, 16943_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26606_C|T, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28690_G|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29335_T|C, 29510_A|C, 29734_29759

Case 58 (XFG): BHR/25020274266/2025


Target: 530 samples Number of changes: 152
BC: XFG.3 + FY.1.4.1 + XFG.3BC BR: 131-132, 136-137 BC BR coord: 26872 - 26873, 27387 - 27388
Direction L1: >> Initial region span: 1-131,132-136,138-152Gap history (edge excluded): 131-138 -> 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.97e-01
Rec. model vs L1: 2.86e-08 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 131 290.226493 NaN NaN NaN * * *
LF.7 58 131 289.964059 281.681666 -227.363333 7.171897e-02 * *
XFG.2 500 131 273.151789 267.357038 -198.714076 4.308892e-08 *
XFG.3.1 87 131 268.035180 261.461788 -186.923576 1.186314e-10 *
XFG.1 14 131 252.185044 246.515339 -157.030678 3.834145e-17 *
LF.7.7.1 188 131 220.837599 205.793623 -75.587245 7.928614e-35 *
LF.7.6 15 131 210.184030 188.345024 -40.690048 2.092949e-42 *
LF.7.3 54 143 208.760913 190.967197 -45.934395 2.874816e-41
LF.7.1.8 44 131 206.589098 184.696931 -33.393863 5.439810e-44 *
LF.7.1 165 131 203.280392 193.079604 -50.159207 2.383104e-40 *
|||||

FY.1.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
FY.1.4.1 41 136 13.108949 NaN NaN NaN * * *
GS.7 16 136 11.905952 11.905952 -13.811904 0.299692 * *
JY.1.1 42 136 11.005410 11.005410 -12.010820 0.121846 * *
XBB.1.22 77 136 10.399274 10.399274 -10.798548 0.066537 * *
BA.2.32 367 136 9.922672 9.922672 -9.845345 0.041378 * *
GV.1 137 136 9.823099 9.823099 -9.646197 0.037441 * *
XBB.1.5.46 613 136 9.547214 9.547214 -9.094428 0.028297 * *
XBB.1.16.15 1675 137 9.529018 8.412148 -6.824296 0.009095 * *
XBB.1.5.10 817 137 9.164369 8.022716 -6.045433 0.006189 * *
LP.8.1 1124 137 8.534839 7.712197 -5.424393 0.004517 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 138 4.08917 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14747_A|G,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25100010185/2025


Target: 530 samples Number of changes: 153
BC: XFG.3 + PR.2 BC BR: 150-151 BC BR coord: 29412 - 29413
Direction L1: >> Initial region span: 1-143,151-153Gap history (edge excluded): 143-151
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.54e-08 Rec. model vs L2: 4.65e-186
Flags: Model_2BP_Bad_L1_opp

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 143 286.186454 NaN NaN NaN * * *
LF.7 58 143 285.971646 274.809638 -203.619276 6.959935e-02 * *
XFG.2 500 143 279.652152 265.062027 -184.124054 4.057271e-06 *
XFG.3.1 87 143 275.423658 266.712656 -187.425311 2.123202e-05 * *
XFG.1 14 143 248.245114 239.534111 -133.068223 3.333246e-17 *
LF.7.6 15 143 206.244100 174.700261 -3.400522 2.319448e-45 *
LF.7.7.1 188 143 204.706097 190.758652 -35.517305 2.188538e-38 *
LF.7.1.8 44 143 202.626179 177.888976 -9.777951 5.633574e-44 *
LF.7.1 165 143 199.315922 186.173883 -26.347767 2.233129e-40 *
LF.7.3 54 143 196.001218 171.264015 3.471970 7.474516e-47 *
|||||

PR.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
PR.2 20 151 10.538285 NaN NaN NaN * * *
EF.2 344 150 10.174713 8.379717 -10.759434 0.115325 * *
NY.6 30 151 9.535464 9.535464 -13.070928 0.366045 * *
LP.8.1.1 2345 151 8.446588 8.446588 -10.893177 0.123070 * *
EG.10.1 101 151 7.656183 7.656183 -9.312367 0.055855 * *
NY.13 463 150 7.250896 5.282981 -4.565963 0.005221 * *
XBB.1.5.30 317 151 5.902512 5.902512 -5.805024 0.009706 * *
LP.8.1 1124 150 5.776128 4.471992 -2.943983 0.002311 * *
BF.7.4 1716 151 5.002369 5.002369 -4.004739 0.003927 * *
MC.13 807 150 4.921771 4.895747 -3.791494 0.003535 * *



Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12885_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29194_T|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25100013134/2025


Target: 530 samples Number of changes: 156
BC: LF.7 + PR.2 BC BR: 153-154 BC BR coord: 29412 - 29413
Direction L1: >> Initial region span: 1-134,154-156Gap history (edge excluded): 134-154
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.60e-08 Rec. model vs L2: 7.59e-229
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 134 273.955316 NaN NaN NaN * * *
XFG.3 480 134 260.226493 247.475452 -142.950903 1.206744e-05 * *
XFG.2 500 134 255.682029 237.143963 -122.287925 3.938701e-10 *
XFG.3.1 87 134 238.035180 225.208799 -98.417597 2.582548e-15 *
XFG.1 14 134 222.185044 209.534111 -67.068223 4.022373e-22 *
LF.7.7.1 188 134 204.751470 186.864095 -21.728191 5.741514e-32 *
LF.7.6 15 134 180.184030 144.700261 62.599478 2.798979e-50 *
LF.7.3 54 146 178.760913 154.023710 43.952580 3.139031e-46
LF.7.1.8 44 134 176.589098 147.888976 56.222049 6.798279e-49 *
LF.7.1 165 134 173.280392 156.173883 39.652233 2.694814e-45 *
|||||

PR.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
PR.2 20 154 10.538285 NaN NaN NaN * * *
EF.2 344 153 10.174713 8.379717 -10.759434 0.115325 * *
NY.6 30 154 9.535464 9.535464 -13.070928 0.366045 * *
LP.8.1.1 2345 154 8.446588 8.446588 -10.893177 0.123070 * *
EG.10.1 101 154 7.656183 7.656183 -9.312367 0.055855 * *
NY.13 463 153 7.250896 5.282981 -4.565963 0.005221 * *
XBB.1.5.30 317 154 5.902512 5.902512 -5.805024 0.009706 * *
LP.8.1 1124 153 5.776128 4.471992 -2.943983 0.002311 * *
BF.7.4 1716 154 5.002369 5.002369 -4.004739 0.003927 * *
MC.13 807 153 4.921771 4.895747 -3.791494 0.003535 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2676_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4230_C|T, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17637_A|G, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28988_28993, 29409_C|T,
29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25020274266/2025


Target: 530 samples Number of changes: 152
BC: XFG.3 + FY.1.4.1 + XFG.3BC BR: 131-132, 136-137 BC BR coord: 26872 - 26873, 27387 - 27388
Direction L1: >> Initial region span: 1-131,132-136,138-152Gap history (edge excluded): 131-138 -> 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.97e-01
Rec. model vs L1: 2.86e-08 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 131 290.226493 NaN NaN NaN * * *
LF.7 58 131 289.964059 281.681666 -227.363333 7.171897e-02 * *
XFG.2 500 131 273.151789 267.357038 -198.714076 4.308892e-08 *
XFG.3.1 87 131 268.035180 261.461788 -186.923576 1.186314e-10 *
XFG.1 14 131 252.185044 246.515339 -157.030678 3.834145e-17 *
LF.7.7.1 188 131 220.837599 205.793623 -75.587245 7.928614e-35 *
LF.7.6 15 131 210.184030 188.345024 -40.690048 2.092949e-42 *
LF.7.3 54 143 208.760913 190.967197 -45.934395 2.874816e-41
LF.7.1.8 44 131 206.589098 184.696931 -33.393863 5.439810e-44 *
LF.7.1 165 131 203.280392 193.079604 -50.159207 2.383104e-40 *
|||||

FY.1.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
FY.1.4.1 41 136 13.108949 NaN NaN NaN * * *
GS.7 16 136 11.905952 11.905952 -13.811904 0.299692 * *
JY.1.1 42 136 11.005410 11.005410 -12.010820 0.121846 * *
XBB.1.22 77 136 10.399274 10.399274 -10.798548 0.066537 * *
BA.2.32 367 136 9.922672 9.922672 -9.845345 0.041378 * *
GV.1 137 136 9.823099 9.823099 -9.646197 0.037441 * *
XBB.1.5.46 613 136 9.547214 9.547214 -9.094428 0.028297 * *
XBB.1.16.15 1675 137 9.529018 8.412148 -6.824296 0.009095 * *
XBB.1.5.10 817 137 9.164369 8.022716 -6.045433 0.006189 * *
LP.8.1 1124 137 8.534839 7.712197 -5.424393 0.004517 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 138 4.08917 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14747_A|G,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25280014848/2025


Target: 530 samples Number of changes: 153
BC: LF.7 + LP.8.1.1 BC BR: 142-143 BC BR coord: 28311 - 28312
Direction L1: >> Initial region span: 1-142,146-153Gap history (edge excluded): 142-146
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.27e-05 Rec. model vs L2: 4.91e-171
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 142 301.218402 NaN NaN NaN * * *
XFG.3 480 142 294.117659 294.117659 -264.235319 8.251049e-04 * *
XFG.2 500 144 269.959325 268.429152 -212.858304 5.747566e-15
XFG.3.1 87 142 263.316547 263.316547 -202.633093 3.451975e-17 *
XFG.1 14 142 247.466411 247.466411 -170.932822 4.513362e-24 *
LF.7.7.1 188 142 213.480793 213.480793 -102.961587 7.852395e-39 *
LF.7.1.4 12 142 206.562754 206.562754 -89.125508 7.795713e-42 *
LF.7.6 15 142 205.465397 205.465397 -86.930793 2.594967e-42 *
LF.7.1.8 44 142 201.847475 201.847475 -79.694950 6.950017e-44 *
LF.7.1 165 144 201.180062 198.561759 -73.123519 2.602127e-45
|||||

LP.8.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1.1 2345 146 12.668692 NaN NaN NaN * * *
NY.13 463 146 12.513693 -6.716280 41.432561 8.607080e-01 * *
LP.8.1 1124 146 11.038925 -8.198516 44.397031 1.949524e-01 * *
PR.2 20 151 10.538285 -13.420215 54.840429 1.054172e-03 *
MC.13 807 146 10.184567 -9.052969 46.105939 8.290997e-02 * *
EF.2 344 150 10.174713 -24.572325 77.144651 1.515402e-08
NY.6 30 151 9.535464 -14.423036 56.846072 3.858739e-04 *
EG.10.1 101 151 7.656183 -37.296826 102.593651 4.509523e-14
KP.3.1.1 12013 146 6.638411 -12.606640 53.213280 2.381559e-03 * *
XBB.1.5.30 317 151 5.902512 -31.680096 91.360192 1.237924e-11



Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|G, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28313_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25280016045/2025


Target: 530 samples Number of changes: 156
BC: LF.7 + PR.2 BC BR: 153-154 BC BR coord: 29412 - 29413
Direction L1: >> Initial region span: 1-133,154-156Gap history (edge excluded): 133-154
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.60e-08 Rec. model vs L2: 7.59e-229
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 133 283.955316 NaN NaN NaN * * *
XFG.3 480 133 270.226493 247.475452 -142.950903 1.206744e-05 * *
XFG.2 500 133 265.682029 237.143963 -122.287925 3.938701e-10 *
XFG.3.1 87 133 248.035180 225.208799 -98.417597 2.582548e-15 *
XFG.1 14 133 232.185044 209.534111 -67.068223 4.022373e-22 *
LF.7.7.1 188 133 214.751470 186.864095 -21.728191 5.741514e-32 *
LF.7.6 15 133 190.184030 161.171016 29.657969 3.979511e-43 *
LF.7.3 54 145 188.760913 154.023710 43.952580 3.139031e-46
LF.7.1.8 44 133 186.589098 147.888976 56.222049 6.798279e-49 *
LF.7.1 165 133 183.280392 156.173883 39.652233 2.694814e-45 *
|||||

PR.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
PR.2 20 154 10.538285 NaN NaN NaN * * *
EF.2 344 153 10.174713 8.379717 -10.759434 0.115325 * *
NY.6 30 154 9.535464 9.535464 -13.070928 0.366045 * *
LP.8.1.1 2345 154 8.446588 8.446588 -10.893177 0.123070 * *
EG.10.1 101 154 7.656183 7.656183 -9.312367 0.055855 * *
NY.13 463 153 7.250896 5.282981 -4.565963 0.005221 * *
XBB.1.5.30 317 154 5.902512 5.902512 -5.805024 0.009706 * *
LP.8.1 1124 153 5.776128 4.471992 -2.943983 0.002311 * *
BF.7.4 1716 154 5.002369 5.002369 -4.004739 0.003927 * *
MC.13 807 153 4.921771 4.895747 -3.791494 0.003535 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2676_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5911_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
14747_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17637_A|G, 18163_A|G, 18326_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27209_A|G, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28475_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28988_28993, 29041_G|A, 29409_C|T,
29510_A|C, 29671_A|G, 29734_29759

Case 58 (XFG): BHR/25280016706/2025


Target: 530 samples Number of changes: 151
BC: JN.1.8.1 + LF.7 BC BR: 5-6 BC BR coord: 941 - 942
Direction L1: << Initial region span: 1-5,6-151Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.97e-131Rec. model vs L2: 1.42e-14
Flags: Model_2BP_Bad_L1_opp

JN.1.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.8.1 1498 5 8.870164 NaN NaN NaN * * *
JN.1.8.2 17 4 8.566187 -1.433813 12.867625 0.000033 * *
JN.2.3 36 4 8.407135 -1.592865 13.185731 0.000029 * *
MC.28.1 17 4 7.771146 -2.228854 14.457708 0.000015 * *
JN.3 321 4 7.761717 -2.238283 14.476565 0.000015 * *
JN.1.8 352 4 7.726793 -2.273207 14.546415 0.000014 * *
LZ.2.1 10 4 7.608627 -2.391373 14.782746 0.000013 * *
MC.17.1 10 4 7.608627 -2.391373 14.782746 0.000013 * *
JN.1.28.1 11 4 7.513317 -2.486683 14.973366 0.000012 * *
LD.1.1 11 4 7.513317 -2.486683 14.973366 0.000012 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 6 315.993193 NaN NaN NaN * * *
XFG.3 480 6 315.966793 315.966793 -293.933586 9.704455e-01 * *
XFG.2 500 6 311.198751 303.660121 -269.320242 4.395189e-06 *
XFG.3.1 87 6 282.157898 282.157898 -226.315796 2.021372e-15 *
XFG.1 14 6 267.211449 267.211449 -196.422899 6.500454e-22 *
LF.7.1.8 44 16 236.949787 231.441999 -124.883998 1.897711e-37
LF.7.1 165 28 234.778805 224.430262 -110.860524 1.713270e-40
LF.7.7.1 188 31 224.840478 206.726282 -75.452563 3.504628e-48
LF.7.6 15 3 212.619381 202.234498 -66.468997 3.932419e-50
LF.7.1.2 26 28 206.014702 195.612183 -53.224366 5.217456e-53



Target sequence

, 241_C|T, 510_518, 670_T|G, 897_C|A, 936_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7164_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9079_A|G, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ263366


Target: 530 samples Number of changes: 155
BC: NM.2 + XFG.3 BC BR: 6-7 BC BR coord: 3037 - 3038
Direction L1: << Initial region span: 1-6,8-155Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.16e-252Rec. model vs L2: 5.69e-09
Flags: Model_2BP_Bad_L1_opp

NM.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NM.2 28 6 11.733311 NaN NaN NaN * * *
LP.7 57 6 11.559075 11.559075 -9.118150 0.839457 * *
KP.2.24 44 6 10.665037 10.665037 -7.330075 0.343009 * *
MC.14 35 6 10.458940 10.458940 -6.917881 0.279431 * *
KP.2.3.13 25 6 9.649415 9.649415 -5.298830 0.124307 * *
KP.3.4 62 6 9.012578 9.012578 -4.025156 0.065875 * *
JN.1.69 32 6 8.997090 8.997090 -3.994179 0.064570 * *
JN.1.18.5 37 6 8.851908 8.851908 -3.703815 0.055855 * *
JN.1.1.6 13 4 8.123635 1.960207 10.079587 0.000057 *
KP.2.11 40 6 8.080799 8.080799 -2.161598 0.025861 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 285.679194 NaN NaN NaN * * *
XFG.2 500 8 256.490665 246.490665 -142.981330 2.103508e-13 *
LF.7 58 8 250.998680 240.998680 -131.997360 8.682951e-16 *
XFG.3.1 87 8 218.998816 208.998816 -67.997631 1.099623e-29 *
XFG.1 14 8 201.981146 191.981146 -33.962292 4.462229e-37 *
LF.7.1 165 21 192.943420 169.563639 10.872723 8.219418e-47
LF.7.7.1 188 35 168.118663 136.953669 76.092663 5.655851e-61
LF.7.1.8 44 21 165.926387 142.524551 64.950898 1.484288e-58
LF.7.7.2 239 21 155.215357 122.565540 104.868919 3.184200e-67
LF.7.3 54 21 154.493004 136.742675 76.514650 4.584544e-61



Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3172_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5581_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8278_T|C, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12534_C|T, 12788_A|G, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14568_T|A, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19518_G|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21762_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26769_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27923_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ263370


Target: 530 samples Number of changes: 150
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 7-8, 9-10 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-7,8-9,11-150Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.67e-02
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 6.37e-221
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 9 7.467971 NaN NaN NaN * * *
MC.36 49 9 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 9 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 9 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 9 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 8 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 9 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 8 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 9 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 9 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 316.228088 NaN NaN NaN * * *
LF.7 58 11 304.248505 307.214112 -274.428224 6.524149e-06 *
XFG.2 500 11 299.421298 302.413148 -264.826297 5.369210e-08 *
XFG.3.1 87 11 272.334253 275.208518 -210.417036 8.221082e-20 *
XFG.1 14 11 255.177861 258.213970 -176.427940 3.420537e-27 *
LF.7.1 165 12 222.566038 215.553253 -91.106506 1.016463e-45 *
LF.7.7.1 188 12 218.986556 211.957879 -83.915759 2.791277e-47 *
LF.7.1.8 44 12 215.721266 208.687865 -77.375731 1.060865e-48 *
LF.7.6 15 12 200.487112 193.523220 -47.046441 2.751593e-55 *
LF.7.3 54 12 197.040048 190.000306 -40.000612 8.103939e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ263399


Target: 530 samples Number of changes: 151
BC: XFG.3 + XBB.2.3 + XFG.3BC BR: 7-8, 10-11 BC BR coord: 3566 - 3567, 4205 - 4206
Direction L1: << Initial region span: 1-7,8-10,12-151Gap history (edge excluded): 7-12 -> 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.48e-08
Rec. model vs L1: 4.63e-13 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

XBB.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.2.3 695 10 10.740845 NaN NaN NaN * * *
LU.2.1.1 49 9 7.467971 -2.532029 11.064059 1.725489e-06 *
MC.36 49 9 7.467971 -2.532029 11.064059 1.725489e-06 *
XBB.1.5.86 101 9 6.744670 -3.255330 12.510659 8.356968e-07 *
FL.13 151 9 6.342511 -3.657489 13.314978 5.601843e-07 *
BA.1.21.1 65 8 6.108827 -13.891173 33.782347 2.010606e-11
BA.5.1.2 2225 9 4.344527 -5.655473 17.310947 7.581270e-08 *
B.1.1.25 541 8 3.989795 -16.010205 38.020411 2.413363e-12
EG.5.1.4 1717 9 3.911457 -6.088543 18.177086 4.907088e-08 *
BA.5.2 49968 9 3.872117 -6.127883 18.255767 4.714679e-08 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 12 316.228088 NaN NaN NaN * * *
LF.7 58 12 304.248505 307.214112 -274.428224 6.524149e-06 *
XFG.2 500 12 299.421298 302.413148 -264.826297 5.369210e-08 *
XFG.3.1 87 12 272.334253 275.208518 -210.417036 8.221082e-20 *
XFG.1 14 12 255.177861 258.213970 -176.427940 3.420537e-27 *
LF.7.1 165 13 222.566038 215.553253 -91.106506 1.016463e-45 *
LF.7.7.1 188 13 218.986556 211.957879 -83.915759 2.791277e-47 *
LF.7.1.8 44 13 215.721266 208.687865 -77.375731 1.060865e-48 *
LF.7.6 15 13 200.487112 193.523220 -47.046441 2.751593e-55 *
LF.7.3 54 13 197.040048 190.000306 -40.000612 8.103939e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4205_G|T, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ271485


Target: 530 samples Number of changes: 136
BC: XFG.3.1 + LF.7.7.1 + XFG.3.1BC BR: 10-11, 14-15 BC BR coord: 4330 - 4331, 7841 - 7842
Direction L1: << Initial region span: 1-10,12-14,15-136Gap history (edge excluded): 10-15 -> 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.25e-03
Rec. model vs L1: 2.18e-15 Rec. model vs L2: 2.10e-60
Flags: Model_2BP_Best

XFG.3.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3.1 87 10 5.990321 None None None * * *
|||||

LF.7.7.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.7.1 188 12 15.074492 NaN NaN NaN * * *
JN.1.41 121 13 9.369512 -10.630488 43.260977 1.511490e-07 *
B.1.587 60 14 6.461167 -42.454172 106.908344 2.280254e-21
BA.1.13 393 14 4.581702 -29.556660 81.113320 9.128136e-16
A.2.5 513 14 4.315235 -48.475964 118.951927 5.540264e-24
P.2 983 14 3.664902 -9.262281 40.524562 5.948242e-07
BE.1.4 990 14 3.657806 -26.342194 74.684388 2.273206e-14
B.1.595 1332 14 3.361074 -26.638926 75.277851 1.684033e-14
BA.5.1.22 4997 14 3.137530 -12.348473 46.696947 2.706566e-08
BQ.1.14 1843 14 3.036361 -26.963639 75.927278 1.216760e-14
|||||

XFG.3.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3.1 87 15 261.526954 NaN NaN NaN * * *
XFG.3 480 5 249.636789 254.612995 -183.225991 2.498050e-06
LF.7 58 15 245.337818 249.087481 -172.174961 9.907240e-09 *
XFG.2 500 15 237.198082 242.988315 -159.976631 2.233201e-11 *
XFG.1 14 15 214.250354 220.078832 -114.157664 2.507502e-21 *
LF.7.7.1 188 12 188.225685 160.951726 4.096548 5.240932e-47
LF.7.3.1 26 15 178.158771 166.018755 -6.037510 8.342218e-45 *
LF.7.1 165 15 177.393614 165.241403 -4.482806 3.824123e-45 *
LF.7.1.8 44 15 168.438655 156.229129 13.541741 4.672385e-49 *
LF.7.9 20 15 164.433830 152.399175 21.201650 1.014357e-50 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 6643_T|C, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ272392


Target: 530 samples Number of changes: 149
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 7-8, 9-10 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-7,8-9,11-149Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.67e-02
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 6.30e-221
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 9 7.467971 NaN NaN NaN * * *
MC.36 49 9 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 9 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 9 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 9 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 8 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 9 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 8 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 9 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 9 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 314.726951 NaN NaN NaN * * *
LF.7 58 11 302.739018 305.704624 -271.409249 6.459233e-06 *
XFG.2 500 11 297.915815 300.907665 -261.815330 5.342431e-08 *
XFG.3.1 87 11 270.847887 273.722152 -207.444304 8.303705e-20 *
XFG.1 14 11 253.668374 256.704482 -173.408964 3.386502e-27 *
LF.7.1 165 12 221.056551 214.043766 -88.087531 1.006349e-45 *
LF.7.7.1 188 12 217.477068 210.448392 -80.896784 2.763504e-47 *
LF.7.1.8 44 12 214.211779 207.178378 -74.356755 1.050309e-48 *
LF.7.6 15 12 198.977624 192.013733 -44.027466 2.724214e-55 *
LF.7.3 54 12 195.530560 188.490818 -36.981636 8.023304e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ263370


Target: 530 samples Number of changes: 150
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 7-8, 9-10 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-7,8-9,11-150Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.67e-02
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 6.37e-221
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 9 7.467971 NaN NaN NaN * * *
MC.36 49 9 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 9 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 9 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 9 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 8 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 9 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 8 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 9 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 9 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 316.228088 NaN NaN NaN * * *
LF.7 58 11 304.248505 307.214112 -274.428224 6.524149e-06 *
XFG.2 500 11 299.421298 302.413148 -264.826297 5.369210e-08 *
XFG.3.1 87 11 272.334253 275.208518 -210.417036 8.221082e-20 *
XFG.1 14 11 255.177861 258.213970 -176.427940 3.420537e-27 *
LF.7.1 165 12 222.566038 215.553253 -91.106506 1.016463e-45 *
LF.7.7.1 188 12 218.986556 211.957879 -83.915759 2.791277e-47 *
LF.7.1.8 44 12 215.721266 208.687865 -77.375731 1.060865e-48 *
LF.7.6 15 12 200.487112 193.523220 -47.046441 2.751593e-55 *
LF.7.3 54 12 197.040048 190.000306 -40.000612 8.103939e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ276205


Target: 530 samples Number of changes: 154
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 9-10, 11-12 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-9,10-11,13-154Gap history (edge excluded): 9-13 -> 11-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.37e-06
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 4.42e-223
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 17.865815 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 11 7.467971 NaN NaN NaN * * *
MC.36 49 11 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 11 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 11 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 11 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 10 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 11 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 10 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 11 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 11 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 13 293.481844 NaN NaN NaN * * *
LF.7 58 13 279.815429 287.949524 -227.899047 1.515144e-06 *
XFG.2 500 13 276.065493 281.917806 -215.835611 3.644670e-09 *
XFG.3.1 87 13 263.968420 270.792602 -193.585203 5.371952e-14 *
XFG.1 14 13 230.366719 236.669155 -125.338309 8.125178e-29 *
LF.7.1 165 14 197.954595 195.098146 -42.196291 7.181436e-47 *
LF.7.7.1 188 14 189.187922 185.381201 -22.762401 4.313889e-51 *
LF.7.1.8 44 14 177.294123 172.846222 2.307556 1.552343e-56 *
LF.7.6 15 14 176.200698 173.686904 0.626193 3.595795e-56 *
LF.7.3 54 14 173.078672 169.208093 9.583814 4.095691e-58 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26842_G|A, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28005_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): OZ277109


Target: 530 samples Number of changes: 155
BC: XFG.3 + KP.4.1.1 + XFG.3BC BR: 3-4, 7-8 BC BR coord: 241 - 242, 2789 - 2790
Direction L1: << Initial region span: 1-3,5-7,8-155Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.89e-02
Rec. model vs L1: 1.32e-08 Rec. model vs L2: 5.57e-212
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.941372 None None None * * *
|||||

KP.4.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.4.1.1 12 5 9.890930 NaN NaN NaN * * *
JN.13 15 5 9.156961 -0.843039 11.686078 0.479505 * *
MC.33 31 5 8.718706 -1.281294 12.562588 0.310367 * *
MD.1 19 5 7.821960 -2.178040 14.356080 0.126186 * *
KP.2 1589 4 7.812810 7.812810 -5.625620 2765.564355 * *
MC.36.2 24 6 7.600059 -10.920705 31.841410 0.000020 * *
KP.2.3.13 25 5 7.547523 -2.452477 14.904954 0.096328 * *
XFJ.1 59 5 7.330428 -2.669572 15.339144 0.077305 * *
LF.9 48 5 6.874145 -3.125855 16.251711 0.049046 * *
LB.1.7.1 97 5 6.864110 -3.135890 16.271781 0.048558 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 307.334080 NaN NaN NaN * * *
LF.7 58 8 295.723596 300.896650 -249.793300 1.142165e-05 * *
XFG.2 500 8 281.982221 284.845246 -217.690493 1.222651e-12 *
XFG.3.1 87 8 275.096664 279.051146 -206.102293 3.720196e-15 *
XFG.1 14 11 256.109583 250.461570 -148.923141 1.425892e-27
LF.7.1 165 17 224.704626 209.311326 -66.622651 1.918089e-45
LF.7.7.1 188 17 215.542400 190.391563 -28.783126 1.164172e-53
LF.7.6 15 17 202.560510 187.479320 -22.958639 6.341911e-55
LF.7.3 54 17 199.324167 194.336739 -36.673478 6.016014e-52
LF.7.2.1 67 17 195.749346 180.075747 -8.151494 3.857176e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3096_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11187_T|C, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15613_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): OZ277275


Target: 530 samples Number of changes: 155
BC: LB.1.3 + LF.7 BC BR: 7-8 BC BR coord: 685 - 686
Direction L1: << Initial region span: 1-3,8-155Gap history (edge excluded): 3-8
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.97e-142Rec. model vs L2: 6.86e-12
Flags: Model_2BP_Bad_L1_opp

LB.1.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LB.1.3 778 3 8.908186 NaN NaN NaN * * *
FL.2.3 614 3 4.892847 -17.217623 50.435246 3.305807e-08 *
XBB.1.5.13 2132 4 2.404054 -0.688856 17.377713 4.990744e-01 * *
BA.4.6 19369 6 1.969609 -8.030391 32.060781 3.239245e-04 *
BA.5.1 53705 7 1.728110 1.728110 12.543781 5.612521e+00 *
BA.4 10442 6 0.589038 -9.410962 34.821924 8.149246e-05 *
BA.2 443141 6 0.155509 -0.347806 16.695611 7.011734e-01 *
BA.2.9 75328 6 0.069722 -0.881665 17.763331 4.127142e-01 *
BA.2.12.1 107150 6 -0.688939 -0.894092 17.788184 4.065697e-01 *
BQ.1.1 36940 7 -0.868500 -0.868500 17.736999 4.168620e-01 *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 8 316.180071 NaN NaN NaN * * *
XFG.3 480 5 309.875086 308.960029 -265.920058 7.318024e-04 *
XFG.2 500 9 306.211341 302.285967 -252.571933 9.235878e-07 *
XFG.1 14 8 289.021195 289.021195 -226.042390 1.601629e-12 *
XFG.3.1 87 8 266.528790 266.528790 -181.057580 2.737026e-22 *
LF.7.1 165 16 243.057180 236.047856 -120.095713 1.584832e-35
LF.7.7.1 188 16 224.543813 208.690917 -65.381834 2.078194e-47
LF.7.7.2 239 16 216.171252 190.766192 -29.532384 3.411596e-55
LF.7.2.1 67 16 213.415984 206.391862 -60.783724 2.083574e-48
LF.7.3 54 16 209.578371 202.523741 -53.047482 4.367779e-50



Target sequence

, 21_C|T, 44_C|T, 88_G|A, 121_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4230_C|T, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 28961_C|T, 29409_C|T, 29510_A|C, 29734_29759,
29762_C|T

Case 58 (XFG): OZ263370


Target: 530 samples Number of changes: 150
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 7-8, 9-10 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-7,8-9,11-150Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.67e-02
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 6.37e-221
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 9 7.467971 NaN NaN NaN * * *
MC.36 49 9 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 9 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 9 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 9 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 8 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 9 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 8 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 9 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 9 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 316.228088 NaN NaN NaN * * *
LF.7 58 11 304.248505 307.214112 -274.428224 6.524149e-06 *
XFG.2 500 11 299.421298 302.413148 -264.826297 5.369210e-08 *
XFG.3.1 87 11 272.334253 275.208518 -210.417036 8.221082e-20 *
XFG.1 14 11 255.177861 258.213970 -176.427940 3.420537e-27 *
LF.7.1 165 12 222.566038 215.553253 -91.106506 1.016463e-45 *
LF.7.7.1 188 12 218.986556 211.957879 -83.915759 2.791277e-47 *
LF.7.1.8 44 12 215.721266 208.687865 -77.375731 1.060865e-48 *
LF.7.6 15 12 200.487112 193.523220 -47.046441 2.751593e-55 *
LF.7.3 54 12 197.040048 190.000306 -40.000612 8.103939e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ282610


Target: 530 samples Number of changes: 152
BC: JN.11 + XFG.2 BC BR: 5-6 BC BR coord: 2067 - 2068
Direction L1: << Initial region span: 1-5,7-152Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.07e-235Rec. model vs L2: 1.16e-23
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 5 9.433251 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 -1.582212 19.164424 1.645304e-05 * *
PL.1.1 12 4 8.235466 -1.764534 19.529067 1.367420e-05 * *
PD.2 21 4 7.675851 -8.934158 33.868317 1.051987e-08 *
KP.4.2.4 22 4 7.629331 -10.408730 36.817461 2.406722e-09 *
KR.1.4 24 4 7.408788 -9.835735 35.671469 4.277060e-09 *
KP.3.1.2 28 4 7.277693 -2.722307 21.444614 5.261997e-06 *
JN.1.69 32 4 7.254637 -2.745363 21.490726 5.132078e-06 *
KP.3.1 1957 5 7.210993 7.210993 1.578014 1.080674e-01 * *
JN.1.50.2 33 4 7.162322 -2.837678 21.675356 4.666972e-06 *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 7 320.737083 NaN NaN NaN * * *
XFG.3 480 8 313.613273 293.613273 -247.226546 7.470942e-12 *
LF.7 58 8 313.571870 293.571870 -247.143740 7.142202e-12 *
XFG.3.1 87 8 281.566276 261.566276 -183.132551 8.999891e-26 *
XFG.1 14 8 264.571728 244.571728 -149.143455 3.744575e-33 *
LF.7.1 165 14 222.566038 201.941555 -63.883111 1.146644e-51
LF.7.7.1 188 14 218.986556 210.385030 -80.770060 5.333910e-48
LF.7.1.8 44 14 215.721266 195.115133 -50.230265 1.245572e-54
LF.7.6 15 14 200.487112 179.880978 -19.761956 3.012260e-61
LF.7.3 54 14 197.040048 176.358064 -12.716127 8.916120e-63



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1684_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13118_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22088_C|T, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ284632


Target: 530 samples Number of changes: 143
BC: BQ.1.1.35 + XFG.3 BC BR: 4-5 BC BR coord: 685 - 686
Direction L1: << Initial region span: 1-4,9-143Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.23e-10
Flags: Model_2BP_Bad_L1_opp

BQ.1.1.35 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BQ.1.1.35 191 4 10.486205 NaN NaN NaN * * *
ET.1 78 3 7.434339 -2.565661 13.131321 0.000002 *
KP.3.1.4 511 7 7.427846 2.741159 2.517682 0.000433 *
XEC.39 155 5 6.963453 3.342570 1.314859 0.000793 * *
LB.1.3.1 292 7 6.759817 2.065162 3.869677 0.000220 *
KP.2.2 1334 7 6.735397 2.058892 3.882216 0.000219 *
MC.16 917 6 6.418927 1.730826 4.538348 0.000158 *
KP.3.1 1957 7 6.411016 1.728378 4.543244 0.000158 *
XEC.2 921 7 6.064512 1.375780 5.248439 0.000111 *
XBC.1 44 4 5.867514 5.867514 -3.735028 0.009902 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 278.075549 NaN NaN NaN * * *
XFG.2 500 9 270.818475 257.964145 -167.928290 3.736299e-07 *
LF.7 58 9 247.857314 242.548371 -137.096742 7.547311e-14 *
XFG.3.1 87 9 233.774196 228.482644 -108.965289 5.880853e-20 *
XFG.1 14 9 187.790145 182.498594 -16.997187 6.286495e-40 *
LF.7.1 165 13 178.996898 171.987574 4.024852 1.713853e-44
LF.7.7.1 188 13 143.224718 127.371822 93.256356 7.173875e-64
LF.7.3.1 26 13 139.050423 132.032423 83.935153 7.578200e-62
JN.1.16.1 466 13 135.350871 128.315666 91.368669 1.845704e-63
LF.7.3 54 13 134.060531 127.005901 93.988198 4.980080e-64



Target sequence

, 241_C|T, 601_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3145_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11083_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15738_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22606_A|G, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A,
28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29762_C|T

Case 58 (XFG): OZ284870


Target: 530 samples Number of changes: 140
BC: LF.7 + HK.13 + LF.7 BC BR: 129-130, 134-135 BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >> Initial region span: 1-129,130-134,135-140Gap history (edge excluded): 129-135 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.55e-03
Rec. model vs L1: 1.02e-15Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 129 279.782631 NaN NaN NaN * * *
XFG.3 480 140 254.107420 255.211820 -172.423641 3.538760e-15
XFG.3.1 87 129 229.930731 242.296025 -146.592049 8.708390e-21 *
XFG.2 500 103 228.717189 237.752784 -137.505569 9.294819e-23
XFG.1 14 103 170.141484 177.670054 -17.340109 7.475788e-49
LF.7.1 165 140 155.652251 149.265249 39.469501 3.447643e-61
LF.7.3.1 26 129 149.543813 144.685647 48.628705 3.535522e-63 *
LF.7.1.8 44 129 145.949746 141.142250 55.715501 1.020656e-64 *
LF.7.9 20 73 145.140273 132.767805 72.464389 2.365020e-68
LF.7.7.1 188 133 142.635628 144.292390 49.415220 2.381810e-63
|||||

HK.13 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
HK.13 165 130 10.169244 NaN NaN NaN * * *
FY.8.1 29 131 9.130739 -0.869261 13.738522 0.000016 * *
FY.4.1 61 131 8.549246 -1.450754 14.901508 0.000009 *
FY.8 23 130 8.410314 8.410314 -4.820627 0.172045 * *
FL.1 118 130 8.290629 8.290629 -4.581259 0.152590 * *
HK.19 25 131 7.758518 -2.241482 16.482963 0.000004 *
XFG.3 480 131 7.718840 -2.281160 16.562320 0.000004 *
HK.8 39 131 7.699095 -2.300905 16.601810 0.000004 *
EG.9.1 32 131 7.183154 -2.816846 17.633692 0.000002 *
EG.5.1.2 69 131 7.065371 -2.934629 17.869258 0.000002 *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 135 8.703627 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21641_G|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G,
22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22883_C|A, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23758_C|T,
23854_C|A, 23948_G|T, 24034_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25273_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28878_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C

Case 58 (XFG): OZ285842


Target: 530 samples Number of changes: 150
BC: JN.11 + LF.7 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,7-150Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.22e-227Rec. model vs L2: 4.18e-08
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -8.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -8.470933 0.618783 * *
PD.2 21 4 7.675851 7.675851 -7.351701 0.353455 * *
KP.4.2.4 22 4 7.629331 7.629331 -7.258661 0.337902 * *
KR.1.4 24 4 7.408788 7.408788 -6.817576 0.271173 * *
KP.3.1.2 28 4 7.277693 7.277693 -6.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -6.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -6.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 7.156197 -6.312394 0.210136 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 7 334.007833 NaN NaN NaN * * *
XFG.3 480 7 333.322187 313.322187 -282.644374 5.015761e-01 * *
XFG.2 500 7 328.181516 309.140532 -274.281065 7.673365e-03 * *
XFG.3.1 87 7 291.566276 271.566276 -199.132551 3.684433e-19 *
XFG.1 14 7 286.429076 266.429076 -188.858152 2.169045e-21 *
LF.7.1 165 13 242.649646 222.025163 -100.050326 1.125698e-40
LF.7.7.1 188 13 228.986556 209.020063 -74.040126 2.531759e-46
LF.7.1.8 44 13 225.721266 205.115133 -66.230265 5.099204e-48
LF.7.6 15 13 210.487112 189.880978 -35.761956 1.233179e-54
LF.7.3.1 26 13 209.990938 189.345583 -34.691167 7.222348e-55



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1096_A|G, 2334_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16475_G|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ263370


Target: 530 samples Number of changes: 150
BC: XFG.3 + LU.2.1.1 + XFG.3BC BR: 7-8, 9-10 BC BR coord: 3566 - 3567, 4188 - 4189
Direction L1: << Initial region span: 1-7,8-9,11-150Gap history (edge excluded): 7-11 -> 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.67e-02
Rec. model vs L1: 2.74e-07 Rec. model vs L2: 6.37e-221
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 12.929009 None None None * * *
|||||

LU.2.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LU.2.1.1 49 9 7.467971 NaN NaN NaN * * *
MC.36 49 9 7.467971 7.467971 -10.935941 1.000000 * *
XBB.1.5.86 101 9 6.744670 6.744670 -9.489341 0.484325 * *
FL.13 151 9 6.342511 6.342511 -8.685022 0.324652 * *
XBB.2.3 695 9 6.202173 6.202173 -8.404347 0.280832 * *
BA.1.21.1 65 8 6.108827 -3.891173 11.782347 0.000012 * *
BA.5.1.2 2225 9 4.344527 4.344527 -4.689053 0.043937 * *
B.1.1.25 541 8 3.989795 -6.010205 16.020411 0.000001 *
EG.5.1.4 1717 9 3.911457 3.911457 -3.822914 0.028439 * *
BA.5.2 49968 9 3.872117 3.872117 -3.744233 0.027324 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 316.228088 NaN NaN NaN * * *
LF.7 58 11 304.248505 307.214112 -274.428224 6.524149e-06 *
XFG.2 500 11 299.421298 302.413148 -264.826297 5.369210e-08 *
XFG.3.1 87 11 272.334253 275.208518 -210.417036 8.221082e-20 *
XFG.1 14 11 255.177861 258.213970 -176.427940 3.420537e-27 *
LF.7.1 165 12 222.566038 215.553253 -91.106506 1.016463e-45 *
LF.7.7.1 188 12 218.986556 211.957879 -83.915759 2.791277e-47 *
LF.7.1.8 44 12 215.721266 208.687865 -77.375731 1.060865e-48 *
LF.7.6 15 12 200.487112 193.523220 -47.046441 2.751593e-55 *
LF.7.3 54 12 197.040048 190.000306 -40.000612 8.103939e-57 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4206_C|T, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16394_C|T, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28805_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): OZ286915


Target: 530 samples Number of changes: 135
BC: XFG.3 + CP.5 + XFG.3 BC BR: 16-17, 26-27 BC BR coord: 7842 - 7843, 11307 - 11308
Direction L1: << Initial region span: 1-16,17-21,35-135Gap history (edge excluded): 16-35 -> 21-35
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.65e-11
Rec. model vs L1: 2.72e-52Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 16 32.463016 None None None * * *
|||||

CP.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
CP.5 75 21 9.955291 NaN NaN NaN * * *
GU.1 74 20 9.843387 -10.014339 46.028679 0.000001 *
XBB.1.5.41 44 20 9.843387 -10.014339 46.028679 0.000001 *
DV.5 17 20 9.312759 1.553633 22.892735 0.118837 * *
BA.5.1.22 4997 26 9.302971 9.302971 7.394059 275.889383 *
BQ.1.13 999 26 9.177364 9.177364 7.645272 242.257207 *
BA.5.2.22 994 26 8.899675 8.899675 8.200651 184.011821 *
BE.1 8190 27 8.627139 6.216802 13.566396 12.553506 *
DN.2 895 26 8.007393 8.007393 9.985213 75.188628 *
BF.7 11554 27 7.718461 6.590511 12.818978 18.265244 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 35 211.076442 NaN NaN NaN * * *
LF.7 58 35 207.482856 193.116410 -76.232819 2.839438e-13 *
XFG.2 500 35 197.290861 182.762504 -55.525009 9.084155e-18 *
XFG.3.1 87 39 191.688029 170.702727 -31.405455 5.256457e-23
XFG.1 14 39 189.636519 163.254528 -16.509056 3.056323e-26
LF.7.7.1 188 39 165.425663 142.106791 25.786418 1.994669e-35
LF.7.1 165 35 156.111811 124.906057 60.187887 6.760920e-43 *
KP.3 769 18 152.632080 162.092837 -14.185675 9.581149e-27
KP.3.1 1957 36 150.309901 120.997031 68.005937 1.354922e-44 *
LF.7.3 54 39 150.119738 105.797158 98.405685 3.393425e-51



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5622_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8818_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11288_11296, 11681_C|T, 11727_G|A, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 17410_C|T, 18163_A|G, 18894_C|T, 19955_C|T,
20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ286929


Target: 530 samples Number of changes: 154
BC: LF.7 + XDD.1.1 + LF.7 BC BR: 141-142, 147-148 BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >> Initial region span: 1-141,143-147,148-154Gap history (edge excluded): 141-148 -> 141-143
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.27e-06
Rec. model vs L1: 1.65e-07Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 141 298.898197 NaN NaN NaN * * *
XFG.3 480 141 297.792045 311.334099 -286.668198 3.706174e+00 * *
XFG.2 500 141 288.893236 302.457353 -268.914705 5.156924e-04 * *
XFG.3.1 87 141 263.743179 276.700095 -217.400191 3.366173e-15 *
XFG.1 14 141 245.223539 258.908693 -181.817386 6.324665e-23 *
LF.7.1 165 141 208.084215 217.262826 -98.525652 5.186135e-41 *
LF.7.6 15 141 205.217225 202.733078 -69.466157 2.538312e-47 *
LF.7.7.1 188 141 202.099682 206.410565 -76.821130 1.001330e-45 *
LF.7.1.8 44 141 197.600079 195.085761 -54.171522 1.208349e-50 *
LF.7.3 54 141 193.829884 191.451098 -46.902196 3.188099e-52 *
|||||

XDD.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XDD.1.1 29 143 13.385163 NaN NaN NaN * * *
JG.3 1482 143 10.138247 0.138247 17.723506 3.896856e-02 * *
HK.3 1830 143 9.256169 -0.743831 19.487662 1.608288e-02 * *
JN.1.3 111 145 8.464940 -16.336019 50.672039 2.727174e-09
XBB.1.5.43 48 145 8.201786 -11.033084 40.066167 5.463533e-07
GK.2.1 255 143 7.855661 -8.235089 34.470179 8.984587e-06 *
BW.1 131 145 7.218843 -12.016026 42.032053 2.050525e-07
XBB.1.16.6 4784 142 6.553074 6.553074 4.893853 2.380748e+01 * *
BA.2.76 427 145 6.030217 -13.204653 44.409305 6.238132e-08
BA.2.36 3016 145 5.869129 -13.366736 44.733472 5.315785e-08
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 148 11.12495 None None None * * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): OZ286968


Target: 530 samples Number of changes: 151
BC: XEK.6 + XFG.3 BC BR: 6-7 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-6,8-151Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.00e-01
Rec. model vs L1: 1.10e-245Rec. model vs L2: 3.00e-09
Flags: Model_1BP_Best

XEK.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.6 23 6 16.273655 NaN NaN NaN * * *
XEK.7 12 6 15.403708 15.403708 -18.807416 0.418952 * *
XEK.2 67 6 15.085032 15.085032 -18.170063 0.304221 * *
XEK.1 88 6 13.684686 13.684686 -15.369373 0.075020 * *
XEK.1.1 11 6 12.997514 12.997514 -13.995028 0.037817 * *
KP.2.3.5 89 6 12.724723 12.724723 -13.449447 0.028725 * *
PF.2.1 37 6 12.259868 12.259868 -12.519735 0.018043 * *
LP.8.1.7 42 6 12.225238 12.225238 -12.450475 0.017422 * *
KP.2.2 1334 7 12.190723 8.722390 -5.444779 0.000523 * *
LF.9 48 6 12.151112 12.151112 -12.302224 0.016163 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 348.462493 NaN NaN NaN * * *
XFG.2 500 8 340.821226 323.282596 -306.565192 2.567919e-07 *
LF.7 58 8 336.350487 326.350487 -312.700975 5.504195e-06 *
XFG.3.1 87 8 304.123042 294.123042 -248.246084 5.566140e-20 *
XFG.1 14 8 287.190678 277.190678 -214.381355 2.459105e-27 *
LF.7.1 165 14 254.384274 243.759791 -147.519582 7.452682e-42
LF.7.7.1 188 14 236.607347 217.165042 -94.330084 2.100152e-53
LF.7.1.8 44 14 224.724215 214.118082 -88.236163 9.995951e-55
LF.7.6 15 14 223.630791 213.024657 -86.049313 3.344042e-55
LF.7.3.1 26 14 222.884140 212.238785 -84.477570 1.525283e-55



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 979_T|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25708_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ287971


Target: 530 samples Number of changes: 144
BC: XFG.3 + XBB.1.16.22 + XFG.3BC BR: 4-5, 8-9 BC BR coord: 896 - 897, 3176 - 3177
Direction L1: << Initial region span: 1-4,5-8,10-144Gap history (edge excluded): 4-10 -> 8-10
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.27e-02
Rec. model vs L1: 3.57e-15 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 4 4.53194 None None None * * *
|||||

XBB.1.16.22 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.1.16.22 25 8 8.182764 NaN NaN NaN * * *
NL.4 115 9 8.012209 4.437504 1.124991 2.363563e-02 * *
GN.1.1 93 8 7.347076 7.347076 -4.694153 4.317105e-01 * *
JN.1.9 576 9 6.174414 2.599710 4.800580 3.753750e-03 * *
AY.71 260 5 5.908262 -0.407936 10.815872 1.850286e-04 *
AY.73 462 5 5.908262 -14.087852 38.175704 2.118802e-10
AY.72 300 5 5.908262 -14.087852 38.175704 2.118802e-10
B.1.1.181 17 5 5.908262 -14.087852 38.175704 2.118802e-10
AY.2 1597 5 5.907009 -21.536087 53.072174 1.238135e-13
AY.38 560 5 5.897490 -14.098624 38.197248 2.097720e-10
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 10 236.270134 NaN NaN NaN * * *
LF.7 58 10 233.697884 228.383026 -110.766052 4.118589e-06 *
XFG.2 500 10 230.267352 224.873192 -103.746384 1.231331e-07 *
XFG.3.1 87 9 229.822136 224.540955 -103.081910 8.808179e-08 *
XFG.1 14 10 182.893469 177.525502 -9.051003 3.361484e-28 *
LF.7.1 165 12 150.222089 147.507258 50.985483 3.083264e-41
LF.7.3.1 26 12 144.392309 130.100918 85.798164 8.513640e-49
LF.7.1.8 44 12 142.683653 128.322753 89.354495 1.442921e-49
LF.7.7.1 188 12 141.151123 128.739889 88.520223 2.185117e-49
LF.7.9 20 12 131.014800 116.828770 112.342460 1.469019e-54



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12116_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22259_A|G, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27887_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ287981


Target: 530 samples Number of changes: 139
BC: JN.1.61 + XFG.2 BC BR: 4-5 BC BR coord: 2067 - 2068
Direction L1: << Initial region span: 1-4,5-139Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.21e-154Rec. model vs L2: 1.46e-16
Flags: Model_2BP_Bad_L1_opp

JN.1.61 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.61 13 4 8.056002 NaN NaN NaN * * *
LF.7.6 15 4 7.912902 7.912902 -3.825803 0.869358 * *
MC.5 19 4 7.676513 7.676513 -3.353026 0.683861 * *
JN.1.9 576 4 7.611185 7.611185 -3.222370 0.640824 * *
XFG.3.1 87 4 7.541338 7.541338 -3.082676 0.597501 * *
KP.3.5 345 4 7.429557 1.360203 9.279594 0.001237 * *
JN.1.40 26 4 7.323635 7.323635 -2.647269 0.481909 * *
XEC.2.3 28 4 7.288747 7.288747 -2.577494 0.465334 * *
KP.3.1.11 31 4 7.186965 -2.161221 16.322441 0.000037 * *
KP.2.27 73 4 7.009846 7.009846 -2.019692 0.351692 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 5 268.451318 NaN NaN NaN * * *
XFG.3 480 3 266.120225 261.420618 -184.841236 8.849318e-04 *
XFG.3.1 87 1 263.645367 256.104029 -174.208058 4.351456e-06
LF.7 58 3 263.284930 258.570676 -179.141352 5.118828e-05 *
XFG.1 14 3 212.337916 207.623663 -77.247325 3.837409e-27
LF.7.1 165 1 184.727660 177.856903 -17.713807 4.519511e-40
LF.7.3.1 26 3 165.604825 160.929792 16.140417 2.016774e-47
LF.7.1.8 44 15 163.998212 158.490423 21.019154 1.757838e-48
LF.7.7.1 188 14 160.364115 148.132389 41.735222 5.567855e-53
LF.7.9 20 3 153.201129 148.486875 41.026250 7.940767e-53



Target sequence

, 241_C|T, 337_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5654_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20404_C|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26029_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): OZ288005


Target: 530 samples Number of changes: 156
BC: JN.1 + XFG.3 BC BR: 13-14 BC BR coord: 3795 - 3796
Direction L1: << Initial region span: 1-12,14-156Gap history (edge excluded): 12-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.90e-06
Rec. model vs L1: 8.74e-98Rec. model vs L2: 1.29e-14
Flags: Model_1BP_Best

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 12 14.844390 NaN NaN NaN * * *
KP.2.3.10 10 6 13.966498 -7.716213 47.432427 3.599702e-10
KP.4.2.4 22 6 13.105203 -16.873398 65.746796 3.785550e-14
XEC.2.1 265 7 12.883972 1.174578 29.650843 2.613030e-06
XEC.2.2.1 46 6 12.719756 -17.254500 66.509000 2.588792e-14
MK.1 151 6 12.429824 -9.293433 50.586866 7.414489e-11
KR.1.4 24 6 11.948497 -16.978736 65.957472 3.408224e-14
JN.11 67 6 11.892484 -23.451718 78.903436 5.280108e-17
KP.3.1.2 28 6 11.663252 -10.019459 52.038918 3.591019e-11
JN.1.69 32 6 11.470297 -10.212414 52.424828 2.969626e-11
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 14 299.641562 NaN NaN NaN * * *
LF.7 58 14 298.103700 298.103700 -266.207400 2.154557e-01 * *
XFG.2 500 14 294.527672 294.527672 -259.055343 6.036083e-03 * *
XFG.3.1 87 14 265.967596 265.967596 -201.935191 2.383992e-15 *
XFG.1 14 14 248.873388 248.873388 -167.746777 8.975127e-23 *
LF.7.1 165 16 215.285288 206.361865 -82.723729 3.083264e-41
LF.7.7.1 188 16 206.607347 188.853086 -47.706173 7.703460e-49
LF.7.1.8 44 16 194.724215 185.800792 -41.601585 3.630080e-50
LF.7.6 15 16 193.630791 184.707368 -39.414735 1.214405e-50
LF.7.3 54 16 190.394448 181.452332 -32.904665 4.685276e-52



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1429_T|C, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3792_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22311_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29362_C|T, 29409_C|T,
29510_A|C, 29734_29759

Case 58 (XFG): OZ288008


Target: 530 samples Number of changes: 144
BC: LD.1 + XFG.3.1 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-144Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.04e-172Rec. model vs L2: 1.35e-07
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LD.1 70 4 9.085704 NaN NaN NaN * * *
XEC.29 135 4 8.457912 8.457912 -8.915824 0.535261 * *
BA.5.1.17 357 3 8.456578 -1.543422 11.086845 0.000024 * *
JN.1.29 69 4 7.971640 7.971640 -7.943281 0.327915 * *
KP.2 1589 5 7.815486 6.243829 -4.487657 0.058426 * *
MC.8 93 4 7.731975 7.731975 -7.463950 0.257947 * *
XEC.39 155 4 7.208205 7.208205 -6.416409 0.153355 * *
MC.9 298 4 6.547233 6.547233 -5.094467 0.078866 * *
MC.2 396 4 6.252566 6.252566 -4.505133 0.059013 * *
MC.1 932 4 6.073660 6.073660 -4.147321 0.049292 * *
|||||

XFG.3.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3.1 87 6 216.104029 NaN NaN NaN * * *
XFG.3 480 6 210.478161 200.478161 -38.956321 3.606563e-03 * *
LF.7 58 6 204.955260 194.955260 -27.910520 1.437529e-05 * *
XFG.2 500 6 193.543640 185.842548 -9.685095 1.589256e-09 *
XFG.1 14 17 167.864152 157.623663 46.752675 8.818679e-22
LF.7.3.1 26 16 134.359234 110.929792 140.140417 4.634711e-42
PY.4 10 16 131.975776 94.360777 173.278445 2.949600e-49
LF.7.1 165 17 130.995405 116.455871 129.088258 1.162786e-39
LF.7.7.1 188 16 130.364115 98.132389 165.735222 1.279538e-47
LF.7.1.8 44 17 122.052452 96.544664 168.910673 2.622386e-48



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 5944_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18912_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21676_C|T, 21711_C|T, 21811_C|T, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26906_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28881_G|A, 28882_G|A,
28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29546_C|T, 29734_29759

Case 58 (XFG): OZ288058


Target: 530 samples Number of changes: 144
BC: XFG.3 + BW.1 + XFG.3 BC BR: 3-4, 5-6 BC BR coord: 896 - 897, 2792 - 2793
Direction L1: << Initial region span: 1-3,4-5,7-144Gap history (edge excluded): 3-7 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.59e-02
Rec. model vs L1: 5.55e-09Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

BW.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BW.1 131 5 8.022833 NaN NaN NaN * * *
BW.1.1.1 116 5 8.022833 8.022833 -12.045667 1.000000 * *
BW.1.1.2 55 5 8.022833 8.022833 -12.045667 1.000000 * *
BW.1.1 210 5 8.008445 8.008445 -12.016889 0.985112 * *
FL.1 118 6 5.310087 3.252149 -2.504297 0.008438 * *
XBB.2.3.19 115 5 4.376513 4.376513 -4.753027 0.025991 * *
XBB.1.5.79 118 5 4.350761 4.350761 -4.701522 0.025349 * *
JY.1.1 42 5 4.285164 4.285164 -4.570327 0.023754 * *
BA.4 10442 5 4.223701 4.223701 -4.447401 0.022371 * *
BA.2.79 46 5 4.194192 4.194192 -4.388384 0.021710 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 283.528307 NaN NaN NaN * * *
XFG.2 500 7 276.945175 271.633794 -197.267588 1.367187e-03 * *
LF.7 58 7 270.781084 265.499903 -184.999806 2.960951e-06 *
XFG.3.1 87 7 264.002856 258.721675 -171.443351 3.364454e-09 *
XFG.1 14 7 207.581325 202.300144 -58.600287 1.056866e-33 *
LF.7.1 165 12 189.445739 182.432323 -18.864645 2.480782e-42
LF.7.1.8 44 16 177.315503 165.379816 15.240367 9.769396e-50
LF.7.7.1 188 12 171.640098 155.779953 34.440094 6.616689e-54
LF.7.3.1 26 16 171.581856 164.253148 17.493704 3.171659e-50
LF.7.9 20 12 158.117910 151.048026 43.903947 5.840201e-56



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2144_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6286_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20238_G|T, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A,
28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ288067


Target: 530 samples Number of changes: 142
BC: XFG.3 + KP.2.3 BC BR: 112-113 BC BR coord: 25216 - 25217
Direction L1: >> Initial region span: 1-112,117-142Gap history (edge excluded): 112-117
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 7.19e-03
Rec. model vs L1: 2.13e-12Rec. model vs L2: 2.91e-105
Flags: Model_1BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 112 204.434040 NaN NaN NaN * * *
XFG.3.1 87 109 197.771630 196.677218 -105.354436 4.264566e-04 *
LF.7 58 112 190.829205 190.829205 -93.658410 1.234308e-06 *
XFG.2 500 138 189.420789 175.301596 -62.603191 2.222441e-13
XFG.1 14 112 161.065352 161.065352 -34.130704 1.460994e-19 *
LF.7.4 15 90 126.270585 107.691824 72.616352 9.642294e-43
LF.7.3.1 26 112 116.688624 116.688624 54.622752 7.813231e-39 *
LF.7.9 20 90 114.674067 104.495420 79.009160 3.950113e-44
LF.7.1 165 90 113.487679 103.272409 81.455183 1.160376e-44
LF.7.1.8 44 138 110.346683 106.082452 75.835097 1.927375e-43
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 117 26.156199 NaN NaN NaN * * *
XFG.3.1 87 117 23.062675 -7.225622 88.451244 8.032020e-11 *
KP.2 1589 114 22.514011 21.740280 30.519441 3.049049e+02 *
BA.2.86.1 1343 117 22.514000 10.425142 53.149716 3.716399e-03 * *
JN.1.7 1974 117 20.286196 1.417127 71.165747 4.540766e-07 *
XFG.1 14 117 20.242476 -20.160215 114.320429 1.937428e-16 *
XFG.3 480 117 20.189990 -10.109868 94.219735 4.486268e-12 *
KP.2.2 1334 117 18.859660 -9.256657 92.513314 1.054890e-11 *
LP.8.1.1 2345 117 18.034668 -1.303536 76.607071 2.991218e-08 *
JN.1.32 436 117 17.998828 -3.390981 80.781963 3.718297e-09 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 17463_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21995_21997, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25445_G|T, 25584_C|T, 26028_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29367_C|T, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ288069


Target: 530 samples Number of changes: 145
BC: XFG.3 + XDD.1.1 + XFG.3BC BR: 133-134, 138-139 BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >> Initial region span: 1-133,135-138,139-145Gap history (edge excluded): 133-139 -> 133-135
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.18e-07
Rec. model vs L1: 1.78e-07 Rec. model vs L2: 6.04e-297
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 133 222.713158 NaN NaN NaN * * *
XFG.2 500 133 211.023960 224.588076 -111.176152 8.589243e-06 *
LF.7 58 133 209.386332 220.511282 -103.022563 1.452223e-07 *
XFG.3.1 87 133 204.279382 217.236298 -96.472595 5.491854e-09 *
XFG.1 14 133 154.875852 168.561007 0.877987 3.985062e-30 *
LF.7.3.1 26 133 124.648534 122.184886 93.630229 2.884220e-50 *
LF.7.1.8 44 133 121.420590 118.906272 100.187455 1.085282e-51 *
LF.7.1 165 133 118.390858 127.569470 82.861060 6.290776e-48 *
LF.7.3 54 133 115.594277 113.215491 111.569019 3.667811e-54 *
LF.7.6 15 133 114.046898 111.562751 114.874498 7.044028e-55 *
|||||

XDD.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XDD.1.1 29 135 11.897939 NaN NaN NaN * * *
JG.3 1482 135 8.733629 -1.266371 20.532743 4.221414e-02 * *
HK.3 1830 135 7.805379 -2.194621 22.389242 1.665575e-02 * *
JN.1.3 111 138 6.944593 -17.857062 53.714123 2.633374e-09
XBB.1.5.43 48 137 6.686486 -12.548384 43.096767 5.302061e-07
GK.2.1 255 135 6.461610 -9.629140 37.258280 9.830704e-06 *
BW.1 131 138 5.680314 -13.573433 45.146867 1.902361e-07
XBB.1.16.6 4784 134 5.042190 5.042190 7.915619 2.310387e+01 * *
XBB.1.16.9 377 138 4.623266 -5.947702 29.895405 3.897520e-04 *
BA.2.76 427 138 4.498727 -14.752670 47.505340 5.845550e-08
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 139 13.542054 None None None * * *



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19273_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21653_T|C, 21711_C|T, 21830_G|A,
21941_G|T, 21987_G|A, 21992_21994, 22016_T|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28467_A|T,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ288088


Target: 530 samples Number of changes: 138
BC: BA.2.86.1 + XFG.3.1 BC BR: 7-8 BC BR coord: 3150 - 3151
Direction L1: << Initial region span: 1-7,8-138Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.17e-04
Rec. model vs L1: 1.90e-99Rec. model vs L2: 1.91e-12
Flags: Model_1BP_Best

BA.2.86.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.2.86.1 1343 7 9.416509 NaN NaN NaN * * *
JN.1 17255 6 6.528453 4.775698 10.448604 9.657698e-03 * *
KP.3.1.1 12013 6 6.209902 4.924620 10.150760 1.122064e-02 * *
XFJ.3 14 3 4.718819 -14.200087 48.400173 5.547992e-11
MC.28.1 17 3 4.718819 -14.200087 48.400173 5.547992e-11
KP.2.14.1 13 3 4.718819 -24.526872 69.053744 1.819891e-15
KP.2.11 40 3 4.718819 -14.200087 48.400173 5.547992e-11
KP.2.10 47 3 4.718819 -14.200087 48.400173 5.547992e-11
KP.1.1.2 12 3 4.718819 -24.179757 68.359513 2.569667e-15
MC.29 54 3 4.718819 -23.971313 67.942626 3.170142e-15
|||||

XFG.3.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3.1 87 8 275.022935 NaN NaN NaN * * *
XFG.3 480 8 269.407538 269.407538 -206.815075 3.642810e-03 * *
LF.7 58 8 263.891557 263.891557 -195.783115 1.459254e-05 * *
XFG.2 500 8 252.472597 252.472597 -172.945193 1.609383e-10 *
XFG.1 14 8 226.542569 226.542569 -121.085137 8.818679e-22 *
LF.7.3.1 26 14 190.504865 179.848698 -27.697395 4.634711e-42
LF.7.7.1 188 14 186.509746 167.051295 -2.102590 1.279538e-47
LF.7.1 165 14 185.063873 174.428577 -16.857154 2.051855e-44
LF.7.9 20 14 178.128088 167.405781 -2.811562 1.824853e-47
LF.7.1.8 44 14 176.080516 165.463569 1.072861 2.622386e-48



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3140_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ296928


Target: 530 samples Number of changes: 154
BC: XEC.2.2.1 + XFG.3 BC BR: 6-7 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-6,9-154Gap history (edge excluded): 6-9
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.47e-01
Rec. model vs L1: 3.27e-226Rec. model vs L2: 1.04e-07
Flags: Model_1BP_Best

XEC.2.2.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2.2.1 46 6 16.305367 NaN NaN NaN * * *
XEC.33 169 6 13.283043 13.283043 -10.566087 4.880122e-02 * *
KP.2.3.8 103 6 12.992899 12.992899 -9.985799 3.651617e-02 * *
JN.1 17255 8 11.613198 8.214080 -0.428160 3.065898e-04 *
JN.1.8.1 1498 7 10.262360 9.645172 -3.290343 1.281146e-03 * *
LF.7.9.3 20 3 7.111420 1.825673 12.348653 5.145362e-07
XFB.3 56 3 6.955858 1.670112 12.659776 4.406566e-07
NY.12.1 17 3 6.912387 -4.824274 25.648547 6.658212e-10
XEL.5 19 3 6.879637 1.593891 12.812218 4.088163e-07
MC.13.2.4 37 3 6.742160 -6.379166 28.758332 1.406144e-10
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 317.866398 NaN NaN NaN * * *
LF.7 58 9 316.350487 296.350487 -250.700975 2.198082e-01 * *
XFG.2 500 9 312.830902 285.292272 -228.584545 3.457378e-06 *
XFG.3.1 87 9 284.123042 264.123042 -186.246084 2.222819e-15 *
XFG.1 14 20 267.431167 247.190678 -152.381355 9.820354e-23
LF.7.1 165 20 240.146539 204.660805 -67.321609 3.323402e-41
LF.7.7.1 188 20 225.786977 187.165042 -32.330084 8.386888e-49
LF.7.1.8 44 20 219.625870 184.118082 -26.236163 3.991849e-50
LF.7.6 15 20 212.805087 183.024657 -24.049313 1.335432e-50
LF.7.1.2 26 20 210.437974 174.898264 -7.796528 3.953475e-54



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 533_G|A, 670_T|G, 897_C|A, 1601_C|T, 2500_A|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4795_C|T, 5239_C|T, 6183_A|G, 7760_G|A,
7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24095_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ296975


Target: 530 samples Number of changes: 156
BC: XFG.3 + XDD.1.1 + XFG.3BC BR: 143-144, 149-150 BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >> Initial region span: 1-143,145-149,150-156Gap history (edge excluded): 143-150 -> 143-145
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.15e-07
Rec. model vs L1: 1.59e-07 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 143 290.889872 NaN NaN NaN * * *
LF.7 58 143 278.898197 290.023147 -240.046294 5.546104e-07 *
XFG.2 500 143 268.893236 282.457353 -224.914705 2.860084e-10 *
XFG.3.1 87 143 243.743179 256.700095 -173.400191 1.866914e-21 *
XFG.1 14 143 225.223539 238.908693 -137.817386 3.507725e-29 *
LF.7.1 165 143 188.084215 197.262826 -54.525652 2.876285e-47 *
LF.7.6 15 143 185.217225 182.733078 -25.466157 1.407774e-53 *
LF.7.7.1 188 143 182.099682 186.410565 -32.821130 5.553480e-52 *
LF.7.1.8 44 143 177.600079 175.085761 -10.171522 6.701627e-57 *
LF.7.3 54 143 173.829884 171.451098 -2.902196 1.768153e-58 *
|||||

XDD.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XDD.1.1 29 145 13.385163 NaN NaN NaN * * *
JG.3 1482 145 10.138247 0.138247 17.723506 3.896856e-02 * *
HK.3 1830 145 9.256169 -0.743831 19.487662 1.608288e-02 * *
JN.1.3 111 147 8.464940 -16.336019 50.672039 2.727174e-09
XBB.1.5.43 48 147 8.201786 -11.033084 40.066167 5.463533e-07
GK.2.1 255 145 7.855661 -8.235089 34.470179 8.984587e-06 *
BW.1 131 147 7.218843 -12.016026 42.032053 2.050525e-07
XBB.1.16.6 4784 144 6.553074 6.553074 4.893853 2.380748e+01 * *
BA.2.76 427 147 6.030217 -13.204653 44.409305 6.238132e-08
BA.2.36 3016 147 5.869129 -13.366736 44.733472 5.315785e-08
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 150 13.542054 None None None * * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19273_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21830_G|A, 21941_G|T, 21987_G|A, 21992_21994, 22016_T|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G,
22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A,
22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): OZ297519


Target: 530 samples Number of changes: 155
BC: XFG.3 + KP.3.1.1 BC BR: 135-136 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-135,137-155Gap history (edge excluded): 135-137
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.14e-03
Rec. model vs L1: 4.97e-15Rec. model vs L2: 2.24e-124
Flags: Model_1BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 135 291.500604 NaN NaN NaN * * *
XFG.2 500 135 286.560164 286.560164 -259.120328 7.154598e-03 * *
LF.7 58 153 281.815826 274.611423 -235.222846 4.621322e-08
XFG.3.1 87 135 239.067128 239.067128 -164.134256 1.689541e-23 *
XFG.1 14 135 223.216992 223.216992 -132.433984 2.209028e-30 *
LF.7.7.1 188 153 205.103504 201.808054 -89.616108 1.117192e-39
LF.7.1 165 135 196.525100 196.525100 -79.050200 5.660849e-42 *
LF.7.1.8 44 135 189.566806 189.566806 -65.133611 5.372693e-45 *
LF.7.6 15 135 181.215978 181.215978 -48.431956 1.270086e-48 *
LF.7.3.1 26 135 174.696536 174.696536 -35.393072 1.871686e-51 *
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 137 16.044568 NaN NaN NaN * * *
JN.1 17255 138 15.166261 -4.833739 59.667477 1.883112e-05 * *
BA.2.86.1 1343 138 8.957968 -11.042032 72.084064 3.802584e-08 *
NL.11 57 146 8.679461 -27.727278 105.454556 2.157125e-15
FU.1 747 153 6.961561 -43.339202 136.678404 3.567525e-22
MC.24 831 138 6.556822 -13.443178 76.886356 3.432421e-09 *
LF.7 58 138 5.993742 -14.006258 78.012517 1.960630e-09 *
LB.1.3 778 142 3.560375 -22.057930 94.115859 6.225204e-13
JN.1.1 3081 142 3.247294 -22.377540 94.755079 4.520426e-13
XFG.3.1 87 142 2.834986 -22.782033 95.564066 3.030132e-13



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1758_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3569_A|G, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27289_G|T,
27373, 27382_G|C, 27383_A|T, 27384_T|C, 27792_27793, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29682_29683, 29693_T|C

Case 58 (XFG): OZ297591


Target: 530 samples Number of changes: 155
BC: BQ.1.10 + XFG.3 BC BR: 8-9 BC BR coord: 2512 - 2513
Direction L1: << Initial region span: 1-4,9-155Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 8.48e-07
Flags: Model_2BP_Bad_L1_opp

BQ.1.10 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BQ.1.10 2048 4 6.071544 NaN NaN NaN * * *
JN.11 67 3 5.085550 -31.287095 88.574190 2.318339e-10 *
KP.2.3.10 10 3 4.790433 -31.582212 89.164424 1.726077e-10 *
DN.3 10 3 4.685073 -48.767248 123.534496 5.938946e-18 *
BF.5.5 91 3 4.661600 -48.338270 122.676541 9.084155e-18 *
PL.1.1 12 3 4.608112 -31.764534 89.529067 1.434550e-10 *
BA.2.75.2 753 4 4.491154 -11.625361 49.250722 8.005831e-02 * *
BN.1.1.1 41 3 4.453366 -45.546634 117.093268 1.486407e-16 *
CM.4 76 3 4.148579 -58.425110 142.850219 3.788128e-22 *
PD.2 21 3 4.048496 -38.934158 103.868317 1.103632e-13 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 297.369129 NaN NaN NaN * * *
XFG.2 500 8 292.061966 291.675165 -241.350330 3.362737e-03 * *
LF.7 58 9 281.650636 281.650636 -221.301272 1.488986e-07 *
XFG.3.1 87 9 249.645042 249.645042 -157.290084 1.876272e-21 *
XFG.1 14 9 232.798710 232.798710 -123.597419 9.069959e-29 *
LF.7.7.1 188 15 194.306068 184.863763 -27.727526 1.379429e-49
LF.7.1 165 15 190.644805 190.020322 -38.040643 2.390492e-47
LF.7.1.8 44 15 183.800033 183.193899 -24.387797 2.596734e-50
LF.7.1.2 26 15 169.255147 168.570572 4.858856 1.155768e-56
LF.7.6 15 15 168.565878 167.959744 6.080511 6.279876e-57



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 684_T|C, 897_C|A, 1263_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11173_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18828_C|T, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27942_C|T, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29645_G|T

Case 58 (XFG): USA/CA-CDPH-500147587/2025


Target: 530 samples Number of changes: 152
BC: FL.29 + XFG.3 BC BR: 3-4 BC BR coord: 1960 - 1961
Direction L1: << Initial region span: 1-3,4-152Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.09e-14
Flags: Model_2BP_Bad_L1_opp

FL.29 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
FL.29 37 3 4.711568 NaN NaN NaN * * *
DS.3 91 3 4.062575 4.062575 1.874850 0.524663 * *
JN.1.42.1 18 3 4.058777 4.058777 1.882447 0.522046 * *
BA.2.86 38 3 3.073585 3.073585 3.852830 0.194952 * *
BA.5.1.30 4775 3 3.037057 3.037057 3.925885 0.187308 * *
BA.5.1.12 592 3 2.876304 2.876304 4.247392 0.159614 * *
HN.8 13 3 2.813097 2.813097 4.373805 0.150318 * *
BN.1.5 1025 3 2.731778 2.731778 4.536444 0.138069 * *
BN.1.3.1 1042 3 2.308064 2.308064 5.383873 0.090718 * *
BA.2.75.2 753 3 1.944050 1.944050 6.111900 0.062976 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 4 284.794795 NaN NaN NaN * * *
XFG.2 500 4 266.630867 259.092237 -170.184474 6.862152e-12 *
LF.7 58 4 259.956453 259.956453 -171.912907 1.629765e-11 *
XFG.3.1 87 4 255.385880 255.385880 -162.771760 1.688104e-13 *
XFG.1 14 4 224.571728 224.571728 -101.143455 6.992216e-27 *
LF.7.7.1 188 10 192.035626 182.593321 -17.186642 4.121962e-45
LF.7.1 165 10 191.785480 191.160997 -34.321995 2.161903e-41
LF.7.1.8 44 33 172.591950 163.169373 21.661254 1.509849e-53
LF.7.6 15 33 163.576197 159.880978 28.238044 5.624770e-55
LF.7.1.2 26 33 162.505401 153.050903 41.898195 6.079579e-58



Target sequence

, 241_C|T, 670_T|G, 1960_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6286_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12469_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24328_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26058_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29249_C|T, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/CA-GBW-GKISBBBE69940/2025


Target: 530 samples Number of changes: 151
BC: LF.7 + NL.11 + LF.7 BC BR: 4-5, 7-8 BC BR coord: 672 - 673, 2789 - 2790
Direction L1: << Initial region span: 1-4,5-7,8-151Gap history (edge excluded): 4-8 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.08e-05
Rec. model vs L1: 1.27e-14Rec. model vs L2: 6.30e-205
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 4 6.259952 None None None * * *
|||||

NL.11 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NL.11 57 5 9.486351 NaN NaN NaN * * *
JN.1.42.2 28 6 8.220027 -1.779973 9.559946 1.281364e-05 * *
MC.10.1.7 11 6 8.092091 -1.907909 9.815817 1.125160e-05 * *
JN.1.15.1 15 6 7.712944 -2.287056 10.574113 7.733106e-06 *
JN.1.13 24 6 7.269373 -2.730627 11.461253 4.955562e-06 *
MH.1 51 6 7.169630 -2.830370 11.660739 4.483978e-06 *
BA.2.26 600 7 6.860964 -13.139036 32.278072 1.493095e-10
MC.13.1 123 6 6.760021 -3.239979 12.479958 2.975793e-06 *
MC.1.2 49 6 6.598166 -3.401834 12.803667 2.535804e-06 *
KP.2.8 51 6 6.558161 -3.441839 12.883678 2.436373e-06 *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 8 339.385844 NaN NaN NaN * * *
XFG.3 480 8 338.775564 344.799659 -347.599318 4.295574e-01 * *
XFG.2 500 8 332.375070 336.310896 -330.621791 8.827973e-05 * *
XFG.3.1 87 8 303.976289 309.017670 -276.035339 1.241551e-16 *
XFG.1 14 8 275.682307 280.040099 -218.080198 3.221889e-29 *
LF.7.1 165 14 247.879235 252.484203 -162.968406 3.476371e-41
LF.7.7.1 188 14 239.084093 233.933701 -125.867402 3.054664e-49
LF.7.1.8 44 14 226.485303 229.533144 -117.066289 3.750315e-51
LF.7.1.2 26 14 220.581658 224.626234 -107.252468 2.764915e-53
PC.3 42 14 218.363457 221.932793 -101.865586 1.876850e-54



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2003_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12256/2025


Target: 530 samples Number of changes: 150
BC: JN.11 + XFG.2 BC BR: 4-5 BC BR coord: 2067 - 2068
Direction L1: << Initial region span: 1-4,5-150Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.51e-229Rec. model vs L2: 8.32e-17
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -2.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -2.470933 0.618783 * *
PD.2 21 4 7.675851 1.065842 11.868317 0.000476 * *
KP.4.2.4 22 4 7.629331 -0.408730 14.817461 0.000109 * *
KR.1.4 24 4 7.408788 0.164265 13.671469 0.000194 * *
KP.3.1.2 28 4 7.277693 7.277693 -0.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -0.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -0.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 0.546188 12.907624 0.000283 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 5 328.815526 NaN NaN NaN * * *
XFG.3 480 1 327.929777 323.397837 -308.795673 4.449338e-03 *
LF.7 58 4 316.567111 312.939756 -287.879512 1.275191e-07 *
XFG.3.1 87 4 284.800151 281.172796 -224.345592 2.042730e-21 *
XFG.1 14 4 269.199060 265.571706 -193.143411 3.412287e-28 *
LF.7.1 165 1 238.824969 232.547938 -127.095876 1.558266e-42
LF.7.1.8 44 4 207.698916 204.118082 -70.236163 7.008895e-55 *
LF.7.7.1 188 11 202.783973 193.341668 -48.683335 1.458663e-59
LF.7.2.1 67 4 193.721203 190.124154 -42.248307 5.857311e-61 *
LF.7.6 15 4 192.551537 188.924182 -39.848364 1.764188e-61 *



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9370_T|C, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14407_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16887_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759, 29762_C|T

Case 58 (XFG): USA/CA-LACPHL-AY12331/2025


Target: 530 samples Number of changes: 157
BC: JN.1.39.1 + XFG.3 BC BR: 7-8 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,12-157Gap history (edge excluded): 4-12
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.55e-208Rec. model vs L2: 1.32e-08
Flags: Model_2BP_Bad_L1_opp

JN.1.39.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.39.1 40 4 10.004107 NaN NaN NaN * * *
KP.2.3 4440 11 8.183088 6.529182 0.941637 6.110447 *
KP.3.1.1 12013 10 8.044589 7.668120 -1.336240 19.105954 *
MC.1.4 125 4 8.028188 2.742441 8.515117 0.138069 * *
JN.1.65.1 46 4 7.964333 2.656608 8.686784 0.126818 * *
KP.4 35 4 7.765644 2.479897 9.040205 0.106459 * *
MC.29 54 4 7.024352 1.738605 10.522790 0.050793 * *
LP.8.1.1 2345 7 6.709351 6.709351 0.581298 7.315534 *
JN.9 55 4 6.041964 0.737868 12.524264 0.018686 * *
NY.7.1 28 4 5.870125 0.548011 12.903978 0.015452 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 12 283.953713 NaN NaN NaN * * *
LF.7 58 12 281.314074 262.377777 -176.755553 7.100535e-02 * *
XFG.2 500 9 271.587245 263.886152 -179.772304 3.198190e-01 *
XFG.3.1 87 12 261.076804 242.157898 -136.315796 1.174510e-10 *
XFG.1 14 12 246.130355 227.211449 -106.422899 3.777062e-17 *
LF.7.7.1 188 18 205.103639 179.552840 -11.105679 7.600648e-38
LF.7.1 165 18 203.360460 184.752458 -21.504917 1.370915e-35
LF.7.1.8 44 18 194.998404 165.462551 17.074897 5.776189e-44
LF.7.6 15 18 191.770351 162.234498 23.531003 2.284916e-45
LF.7.3 54 18 188.534008 158.922305 30.155390 8.302024e-47



Target sequence

, 21_C|T, 44_C|T, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3049_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G,
7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12367/2025


Target: 530 samples Number of changes: 156
BC: XFG.3 + BA.2.38 + XFG.3BC BR: 145-146, 150-151 BC BR coord: 28361 - 28362, 28883 - 28884
Direction L1: >> Initial region span: 1-145,146-150,154-156Gap history (edge excluded): 145-154 -> 150-154
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.19e-05
Rec. model vs L1: 4.09e-13 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 145 266.186454 NaN NaN NaN * * *
LF.7 58 145 265.971646 255.442099 -166.884199 7.171897e-02 * *
XFG.2 500 145 259.041385 250.951004 -157.902009 8.047330e-04 * *
XFG.3.1 87 145 243.919801 235.222221 -126.444442 1.186314e-10 *
XFG.1 14 145 228.245114 220.275772 -96.551544 3.834145e-17 *
LF.7.1 165 145 201.087613 188.629965 -33.259930 6.924999e-31 *
LF.7.6 15 145 186.244100 162.105457 19.789086 2.092949e-42 *
LF.7.7.1 188 145 184.706097 167.362483 9.275033 4.008446e-40 *
LF.7.1.8 44 145 182.626179 158.457365 27.085271 5.439810e-44 *
LF.7.3 54 145 176.001218 151.967935 40.064129 8.302024e-47 *
|||||

BA.2.38 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.2.38 911 150 9.861020 NaN NaN NaN * * *
XBB.1.42 71 146 7.808425 -0.537078 15.074157 3.058503e-05 *
XBB.1.5.33 820 150 6.914078 6.914078 0.171844 5.260206e-02 * *
JD.1 35 146 6.723997 -1.621506 17.243012 1.033474e-05 *
HN.3.1 55 146 6.272012 -2.073491 18.146982 6.556852e-06
AD.2 3211 146 6.011670 -2.336637 18.673275 5.055671e-06
XBB.1.5.85 30 146 5.779536 -2.565968 19.131935 4.016900e-06
AY.109 471 146 5.075648 -35.961016 85.922033 1.260744e-20
JN.1.32 436 146 5.049001 -3.296502 20.593005 1.935780e-06
MC.23 64 146 5.021850 -3.323653 20.647307 1.878569e-06
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 154 8.279257 None None None * * *



Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28817_G|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12442/2025


Target: 530 samples Number of changes: 153
BC: KP.3.1.1 + XFG.3 BC BR: 10-11 BC BR coord: 3773 - 3774
Direction L1: << Initial region span: 1-9,11-153Gap history (edge excluded): 9-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.37e-05
Rec. model vs L1: 1.73e-128Rec. model vs L2: 9.81e-15
Flags: Model_1BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 9 13.231814 NaN NaN NaN * * *
JN.1 17255 9 12.499233 9.829579 6.340841 8.374323e-02 * *
JN.1.65 124 9 9.792360 -0.207640 26.415280 3.652860e-06 *
JN.1.11.1 226 4 9.089588 -2.624465 31.248930 3.264464e-07
KP.1.1 593 4 8.164083 -3.549315 33.098629 1.294463e-07
MC.42 84 9 7.714779 -2.285221 30.570442 4.586401e-07 *
LP.8.1.1 2345 4 6.795103 0.039528 25.920945 4.690366e-06
JN.1.8.1 1498 9 5.526092 -4.473908 34.947815 5.132951e-08 *
LF.7.3.5 16 3 4.718819 -16.963892 59.927783 1.932098e-13
LD.2 13 3 4.718819 -31.985883 89.971766 5.793299e-20
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 11 268.953360 NaN NaN NaN * * *
XFG.1 14 11 258.818365 258.818365 -185.636729 3.966664e-05 * *
LF.7 58 11 253.575487 253.575487 -175.150973 2.091948e-07 *
XFG.2 500 11 242.250753 242.250753 -152.501507 2.524445e-12 *
XFG.3.1 87 11 234.418810 234.418810 -136.837620 1.003784e-15 *
LF.7.7.1 188 13 189.730052 171.975791 -11.951581 7.622916e-43
LF.7.1 165 13 185.651765 176.728342 -21.456685 8.855058e-41
LF.7.1.2 26 13 170.026899 161.103475 9.793049 1.449907e-47
LF.7.1.8 44 13 165.758332 156.834909 18.330182 2.027228e-49
LF.7.6 15 13 162.464213 153.540790 24.918419 7.514539e-51



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1169_T|C, 2344_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3773_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20320_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22595_A|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23371_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29200_C|T, 29409_C|T, 29510_A|C, 29651_G|T, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12607/2025


Target: 530 samples Number of changes: 153
BC: KP.2.3.10 + LF.7 BC BR: 5-6 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-5,7-153Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.89e-01
Rec. model vs L1: 4.17e-212Rec. model vs L2: 5.56e-08
Flags: Model_1BP_Best

KP.2.3.10 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.10 10 5 10.375656 NaN NaN NaN * * *
JN.11 67 5 10.021428 10.021428 -10.042857 0.701173 * *
KP.4.2.4 22 5 9.715032 9.715032 -9.430064 0.516851 * *
PL.1.1 12 5 9.317865 9.317865 -8.635731 0.348192 * *
XEC.2.2.1 46 5 9.173366 9.173366 -8.346733 0.301194 * *
KR.1.4 24 5 9.050803 9.050803 -8.101605 0.265803 * *
MK.1 151 5 8.914620 8.914620 -7.829239 0.232236 * *
JN.1.69 32 5 8.860284 8.860284 -7.720569 0.219808 * *
KP.3.1.2 28 5 8.765557 8.765557 -7.531114 0.199888 * *
LB.1.4.1 74 5 8.648070 8.648070 -7.296139 0.178173 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 7 305.098200 NaN NaN NaN * * *
XFG.2 500 6 299.104506 291.565876 -241.131752 2.915876e-02 * *
XFG.3 480 7 293.171216 283.171216 -224.342433 6.589718e-06 *
XFG.3.1 87 7 259.640359 249.640359 -157.280718 1.807061e-20 *
XFG.1 14 18 257.861264 247.620775 -153.241550 2.397165e-21
LF.7.1 165 23 223.177472 202.427688 -62.855377 5.674536e-41
LF.7.1.8 44 23 216.438824 184.118082 -26.236163 6.338674e-49
LF.7.7.1 188 23 208.776556 184.706634 -27.413269 1.137786e-48
LF.7.6 15 23 195.517566 168.924182 4.151636 1.595489e-55
LF.7.1.2 26 23 194.393647 162.040983 17.918034 1.632211e-58



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4222_A|G, 4321_C|T, 5239_C|T, 6183_A|G, 6312_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8326_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12732/2025


Target: 530 samples Number of changes: 159
BC: XFG.2 + BE.5 BC BR: 153-154 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-148,156-159Gap history (edge excluded): 148-156
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.62e-14 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

XFG.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 148 253.255377 NaN NaN NaN * * *
XFG.3 480 148 248.327684 243.590481 -139.180962 7.226503e-03 * *
LF.7 58 148 247.650734 242.913531 -137.827062 3.679421e-03 * *
XFG.3.1 87 148 225.352179 220.614975 -93.229951 7.603481e-13 *
XFG.1 14 148 208.014349 203.277146 -58.554292 2.240506e-20 *
LF.7.1 165 148 181.692471 176.937031 -5.874061 8.147597e-32 *
LF.7.6 15 148 167.383881 162.646678 22.706644 5.069456e-38 *
LF.7.7.1 188 148 164.543438 159.806235 28.387530 2.961863e-39 *
LF.7.1.8 44 148 161.921450 157.184246 33.631507 2.156321e-40 *
LF.7.3 54 148 155.754705 151.017502 45.964997 4.531980e-43 *
|||||

BE.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BE.5 231 156 7.549258 NaN NaN NaN * * *
BF.38 60 157 7.093101 -22.906899 59.813797 2.880389e-05 * *
BQ.1.1.5 1362 157 7.023821 -13.289818 40.579637 4.317105e-01 * *
FY.6 11 157 6.947943 -23.052057 60.104113 2.491601e-05 * *
JN.1.1 3081 150 6.733092 1.471920 11.056161 1.110144e+06 *
PG.3 31 157 6.524418 -29.673996 73.347993 3.305807e-08 *
FY.3.3 33 157 6.508577 -23.491423 60.982846 1.604682e-05 * *
BQ.1.1.74 24 157 6.486239 -23.513761 61.027523 1.565062e-05 * *
XBB.1.5.25 43 157 6.222814 -23.777186 61.554373 1.206744e-05 * *
XEC.2 921 156 6.120054 -4.495483 22.990967 2.849788e+03 * *



Target sequence

, 21_C|T, 44_C|T, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 14895_T|C, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21411_C|T, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29543_G|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12742/2025


Target: 530 samples Number of changes: 151
BC: XFG.3 + JJ.1 + XFG.3 BC BR: 5-6, 8-9 BC BR coord: 2335 - 2336, 3430 - 3431
Direction L1: << Initial region span: 1-4,6-8,9-151Gap history (edge excluded): 4-9 -> 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.47e-02
Rec. model vs L1: 1.19e-08Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 4 6.540343 None None None * * *
|||||

JJ.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JJ.1 58 6 9.078968 NaN NaN NaN * * *
JN.2.3 36 6 6.260055 6.260055 -4.520111 5.960594e-02 * *
XBB.1.5.3 150 6 5.526086 5.526086 -3.052172 2.858137e-02 * *
KP.2.3.5 89 6 5.354938 5.354938 -2.709876 2.411310e-02 * *
XEC.8 592 6 5.251827 5.251827 -2.503654 2.170962e-02 * *
B.1.260 81 8 5.061178 -5.066705 18.133410 7.192909e-07
B.1.1.70 669 7 4.898144 -5.101856 18.203713 6.945512e-07 *
XBB.1.5.14 241 6 4.354619 -2.070485 12.140970 1.437529e-05 * *
MC.24 831 6 4.217147 4.217147 -0.434294 7.711828e-03 * *
BA.5.9 2618 6 4.166044 4.166044 -0.332088 7.335718e-03 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 315.853318 NaN NaN NaN * * *
LF.7 58 9 311.671369 308.339398 -272.678795 1.733548e-02 * *
XFG.2 500 9 300.299960 295.867638 -247.735275 6.657079e-08 *
XFG.3.1 87 18 293.143640 289.059389 -234.118778 7.340713e-11
XFG.1 14 18 277.431167 271.756651 -199.513302 2.240125e-18
LF.7.1 165 18 239.522535 219.125767 -94.251533 3.114251e-41
LF.7.7.1 188 18 235.786977 211.782230 -79.564460 2.011225e-44
LF.7.6 15 18 222.805087 208.437928 -72.875856 7.127170e-46
LF.7.1.2 26 18 220.437974 199.761489 -55.522978 1.211270e-49
LF.7.3 54 18 219.568744 204.413895 -64.827790 1.273157e-47



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1784_G|A, 2790_C|T, 3037_C|T, 3095_T|C, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4354_G|A, 5239_C|T, 6183_A|G, 7777_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28372_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY12924/2025


Target: 530 samples Number of changes: 155
BC: JN.11 + LF.7 BC BR: 8-9 BC BR coord: 2792 - 2793
Direction L1: << Initial region span: 1-4,13-155Gap history (edge excluded): 4-13
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.59e-229Rec. model vs L2: 4.10e-08
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
LP.8.1 1124 5 8.478730 -7.425220 36.850441 356824.734345 * *
KP.2.3.10 10 4 8.417788 -20.505004 63.010008 0.744532 * *
PL.1.1 12 4 8.235466 -20.687326 63.374651 0.621885 * *
PD.2 21 4 7.675851 -27.856950 77.713901 0.000478 * *
KP.4.2.4 22 4 7.629331 -29.331522 80.663045 0.000109 * *
KR.1.4 24 4 7.408788 -28.758527 79.517053 0.000194 * *
KP.3.1.2 28 4 7.277693 -21.645099 65.290198 0.238115 * *
JN.1.69 32 4 7.254637 -21.668155 65.336310 0.232236 * *
JN.1.50.2 33 4 7.162322 -21.760470 65.520940 0.212248 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 13 296.767482 NaN NaN NaN * * *
XFG.3 480 13 284.946380 282.104480 -226.208959 7.138556e-06 *
XFG.2 500 13 280.776755 278.012828 -218.025655 1.194940e-07 *
XFG.3.1 87 13 251.484913 248.563151 -159.126302 1.938088e-20 *
XFG.1 14 13 235.397068 232.637149 -127.274299 2.339173e-27 *
LF.7.1 165 15 201.503267 189.801576 -41.603152 5.835233e-46
LF.7.1.8 44 15 194.724215 183.040874 -28.081747 6.764373e-49
LF.7.7.1 188 15 192.783973 172.264460 -6.528919 1.414831e-53
LF.7.6 15 15 179.530316 167.846974 2.306052 1.702640e-55
LF.7.3 54 15 176.188613 164.429420 9.141160 5.597669e-57



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1238_C|T, 1844_A|C, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3569_A|G, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27630_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29422_G|A, 29510_A|C, 29682_29683, 29693_T|C,
29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13064/2025


Target: 530 samples Number of changes: 155
BC: KP.3.1.1 + XFG.3 BC BR: 11-12 BC BR coord: 3773 - 3774
Direction L1: << Initial region span: 1-10,12-155Gap history (edge excluded): 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.76e-05
Rec. model vs L1: 9.76e-129Rec. model vs L2: 1.27e-14
Flags: Model_1BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 10 14.815722 NaN NaN NaN * * *
JN.1 17255 10 13.427482 10.757828 12.484345 4.349975e-02 * *
JN.1.65 124 10 10.554287 0.554287 32.891426 1.608835e-06 *
JN.1.11.1 226 5 10.475037 -1.239016 36.478032 2.672717e-07
KP.1.1 593 5 9.615892 -2.097506 38.195012 1.130993e-07
MC.42 84 10 8.930710 -1.069290 36.138581 3.167985e-07 *
LP.8.1.1 2345 5 8.231787 1.476211 31.047579 4.037035e-06
XEC.35.1 28 4 7.305296 -20.777145 75.554290 8.770216e-16
LF.7.1.11 20 4 7.236303 -27.355280 88.710561 1.217174e-18
NC.1.2.1 10 4 7.236303 -31.841643 97.683285 1.372593e-20
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 12 273.648542 NaN NaN NaN * * *
XFG.1 14 12 262.294685 262.294685 -188.589370 1.171079e-05 * *
LF.7 58 12 257.422181 257.422181 -178.844361 8.941298e-08 *
XFG.2 500 12 246.001670 246.001670 -156.003341 9.812001e-13 *
XFG.3.1 87 12 238.901493 238.901493 -141.802986 8.095930e-16 *
LF.7.7.1 188 14 193.553426 175.799165 -15.598331 3.193633e-43
LF.7.1 165 14 189.433786 180.510363 -25.020726 3.546598e-41
LF.7.1.2 26 14 172.884180 163.960757 8.078487 2.302705e-48
LF.7.6 15 14 166.564688 157.641265 20.717470 4.144739e-51
LF.7.3 54 14 163.328345 154.386230 27.227540 1.599074e-52



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1169_T|C, 2344_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3773_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20320_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22595_A|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23371_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29200_C|T, 29409_C|T, 29510_A|C,
29651_G|T, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13080/2025


Target: 530 samples Number of changes: 155
BC: XFG.3 + XBB.1.16.22 + XFG.3BC BR: 4-5, 8-9 BC BR coord: 896 - 897, 3176 - 3177
Direction L1: << Initial region span: 1-4,5-8,9-155Gap history (edge excluded): 4-9 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.02e-10
Rec. model vs L1: 3.56e-15 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 4 4.53194 None None None * * *
|||||

XBB.1.16.22 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.1.16.22 25 8 8.182764 NaN NaN NaN * * *
GN.1.1 93 8 7.347076 7.347076 -4.694153 4.317105e-01 * *
AY.73 462 5 5.908262 -14.087852 38.175704 2.118802e-10
AY.71 260 5 5.908262 -0.407936 10.815872 1.850286e-04 *
AY.72 300 5 5.908262 -14.087852 38.175704 2.118802e-10
B.1.1.181 17 5 5.908262 -14.087852 38.175704 2.118802e-10
AY.2 1597 5 5.907009 -21.536087 53.072174 1.238135e-13
AY.38 560 5 5.897490 -14.098624 38.197248 2.097720e-10
AY.74 544 5 5.897171 -3.465409 16.930818 8.719052e-06
AY.29.2 32 5 5.843723 -14.152391 38.304781 1.995413e-10
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 294.248491 NaN NaN NaN * * *
LF.7 58 9 285.286785 280.005604 -214.011208 7.016509e-09 *
XFG.2 500 9 281.759859 276.448478 -206.896956 2.005415e-10 *
XFG.3.1 87 9 253.041948 247.760767 -149.521534 6.954974e-23 *
XFG.1 14 9 236.109583 230.828403 -115.656805 3.088090e-30 *
LF.7.1 165 15 204.215007 199.856741 -53.713482 1.089980e-43
LF.7.7.1 188 15 195.542400 181.508428 -17.016856 1.175672e-51
LF.7.1.8 44 15 183.653934 167.686297 10.627406 1.164568e-57
LF.7.6 15 15 182.560510 166.662382 12.675236 4.178429e-58
LF.7.3 54 15 179.324167 163.331496 19.337008 1.495590e-59



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5184_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16329_C|T, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20679_G|T,
21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22525_A|G, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13088/2025


Target: 530 samples Number of changes: 155
BC: BA.2.76 + XFG.3 BC BR: 4-5 BC BR coord: 672 - 673
Direction L1: << Initial region span: 1-4,7-155Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.63e-13
Flags: Model_2BP_Bad_L1_opp

BA.2.76 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.2.76 427 4 4.529835 NaN NaN NaN * * *
KP.3.1.1 12013 5 3.256950 -0.356743 8.713486 0.007559 * *
BF.14 1581 4 3.190337 3.190337 1.619326 0.261846 * *
KP.2.3 4440 6 2.973530 -0.854327 9.708655 0.004585 *
BQ.1.1.10 705 4 2.831446 2.831446 2.337108 0.182684 * *
LP.8.1.1 2345 5 2.630623 -0.968622 9.937244 0.004087 * *
B.1.349 537 3 1.593554 -8.406446 24.812891 0.000002 *
B.1.1.7 477665 3 1.434268 -8.565732 25.131465 0.000002 *
BE.1.1.2 2143 4 1.170904 1.170904 5.658191 0.034735 * *
BA.5 6418 4 0.522220 0.522220 6.955560 0.018133 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 276.923940 NaN NaN NaN * * *
LF.7 58 7 272.735071 266.362426 -180.724851 1.529851e-02 * *
XFG.2 500 7 261.371004 257.283167 -162.566334 1.751567e-06 *
XFG.3.1 87 7 254.123042 247.750397 -143.500793 1.265986e-10 *
XFG.1 14 7 237.190678 230.818032 -109.636065 5.621124e-18 *
LF.7.7.1 188 15 195.542400 170.754452 10.491096 4.612380e-44
LF.7.1 165 15 193.591003 188.598160 -25.196321 2.593643e-36
LF.7.6 15 15 182.560510 166.652011 18.695977 7.605824e-46
LF.7.3 54 15 179.324167 163.339818 25.320364 2.777356e-47
LF.7.1.2 26 15 174.512558 158.486398 35.027204 2.163375e-49



Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T,
29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13108/2025


Target: 530 samples Number of changes: 156
BC: KP.2 + XFG.3 BC BR: 11-12 BC BR coord: 4188 - 4189
Direction L1: << Initial region span: 1-11,18-156Gap history (edge excluded): 11-18
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.83e-111Rec. model vs L2: 6.48e-19
Flags: Model_2BP_Bad_L1_opp

KP.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2 1589 11 19.833322 NaN NaN NaN * * *
KP.2.3 4440 11 14.388256 14.388256 -0.776512 4.317840e-03 * *
MC.1 932 9 14.268497 5.345074 17.309852 5.094164e-07
KP.3.1.4 511 9 14.077741 5.154318 17.691364 4.212666e-07
KP.3.1.1 12013 9 12.914215 3.990376 20.019249 1.314026e-07
JN.1 17255 11 12.855362 12.855362 2.289275 9.303032e-04 * *
KP.2.2 1334 9 12.162400 3.238977 21.522046 6.207019e-08
JN.1.7 1974 9 11.375845 2.451915 23.096170 2.817023e-08
JN.1.4.5 1757 9 9.356603 0.433180 27.133640 3.755667e-09
LD.1 70 4 9.085704 -20.263175 68.526350 3.844070e-18
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 18 244.192233 NaN NaN NaN * * *
LF.7 58 18 242.885348 239.565012 -145.130025 3.456202e-02 * *
XFG.2 500 18 234.896342 228.240279 -122.480558 4.170749e-07 *
XFG.3.1 87 18 228.660957 220.408336 -106.816672 1.658396e-10 *
XFG.1 14 18 213.954846 204.320491 -74.640982 1.705651e-17 *
LF.7.1 165 18 175.740514 150.879263 32.241474 1.054855e-40 *
LF.7.7.1 188 18 171.963602 152.783973 28.432055 7.088004e-40 *
LF.7.1.8 44 18 167.680110 142.778456 48.443088 3.201899e-44 *
LF.7.6 15 18 158.704612 139.530316 54.939368 1.241511e-45 *
LF.7.1.2 26 18 157.580693 132.725558 68.548884 1.375868e-48 *



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3951_3953, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 6268_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18048_T|C, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22082_C|T, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T,
29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13110/2025


Target: 530 samples Number of changes: 155
BC: BA.2.76 + XFG.3 BC BR: 4-5 BC BR coord: 672 - 673
Direction L1: << Initial region span: 1-4,7-155Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.63e-13
Flags: Model_2BP_Bad_L1_opp

BA.2.76 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.2.76 427 4 4.529835 NaN NaN NaN * * *
KP.3.1.1 12013 5 3.256950 -0.356743 8.713486 0.007559 * *
BF.14 1581 4 3.190337 3.190337 1.619326 0.261846 * *
KP.2.3 4440 6 2.973530 -0.854327 9.708655 0.004585 *
BQ.1.1.10 705 4 2.831446 2.831446 2.337108 0.182684 * *
LP.8.1.1 2345 5 2.630623 -0.968622 9.937244 0.004087 * *
B.1.349 537 3 1.593554 -8.406446 24.812891 0.000002 *
B.1.1.7 477665 3 1.434268 -8.565732 25.131465 0.000002 *
BE.1.1.2 2143 4 1.170904 1.170904 5.658191 0.034735 * *
BA.5 6418 4 0.522220 0.522220 6.955560 0.018133 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 262.228759 NaN NaN NaN * * *
LF.7 58 7 258.888377 252.515732 -155.031463 3.579311e-02 * *
XFG.2 500 7 247.620087 243.532250 -137.064500 4.483978e-06 *
XFG.3.1 87 7 239.640359 233.267714 -116.535427 1.569647e-10 *
XFG.1 14 7 223.714357 217.341712 -84.683424 1.894484e-17 *
LF.7.7.1 188 15 181.719025 156.931077 36.137845 1.100934e-43
LF.7.1 165 15 179.808982 174.816139 0.367721 6.443445e-36
LF.7.1.8 44 15 171.708175 155.753157 38.493687 3.399893e-44
LF.7.6 15 15 168.460035 152.551537 44.896926 1.378959e-45
LF.7.3 54 15 165.118331 149.133983 51.732035 4.533523e-47



Target sequence

, 174_G|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10450_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20235_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13111/2025


Target: 530 samples Number of changes: 157
BC: KP.3.1 + XFG.2 BC BR: 11-12 BC BR coord: 4188 - 4189
Direction L1: << Initial region span: 1-11,15-157Gap history (edge excluded): 11-15
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.41e-118Rec. model vs L2: 4.68e-21
Flags: Model_2BP_Bad_L1_opp

KP.3.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1 1957 11 15.749998 NaN NaN NaN * * *
KP.2.2 1334 11 15.576007 15.576007 -7.152014 8.394570e-01 * *
LF.7.7.1 188 9 15.101403 -2.652858 29.305717 1.015804e-08
LB.1.3.1 292 9 14.642740 5.715886 12.568227 4.383842e-05 *
XEC.2 921 11 14.555106 14.555106 -5.110211 3.027040e-01 * *
KP.3.1.1 12013 11 14.550812 14.550812 -5.101624 3.011942e-01 * *
JN.1.11.1 226 9 13.983183 5.059760 13.880480 2.277152e-05 *
XFG.3 480 12 13.775049 5.834013 12.331975 4.942768e-05 * *
MC.24 831 9 13.219225 4.295802 15.408395 1.059636e-05 *
JN.1 17255 11 13.142408 13.142408 -2.284817 7.353454e-02 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 15 275.120321 NaN NaN NaN * * *
LF.7 58 15 271.173162 257.027123 -180.054246 2.322758e-03 * *
XFG.3 480 15 270.626033 258.567070 -183.134140 1.083471e-02 * *
XFG.3.1 87 15 236.922525 224.891019 -115.782037 2.570105e-17 *
XFG.1 14 15 233.734736 221.703229 -109.406459 1.063464e-18 *
LF.7.1 165 23 196.959492 165.285288 3.429425 3.340629e-43
LF.7.7.1 188 15 186.607347 156.607347 20.785305 5.677434e-47 *
LF.7.1.8 44 23 176.438824 144.724215 44.551569 3.933088e-52
LF.7.6 15 15 173.630791 143.630791 46.738419 1.315774e-52 *
LF.7.3 54 15 170.394448 140.394448 53.211105 5.178912e-54 *



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3717_C|T, 4184_G|A, 4214_T|C, 4222_A|G, 4255_G|A, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8326_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 13620_C|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26196_G|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27765_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13137/2025


Target: 530 samples Number of changes: 158
BC: LD.1 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,21-158Gap history (edge excluded): 4-21
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.19e-197Rec. model vs L2: 1.33e-07
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LD.1 70 4 9.085704 NaN NaN NaN * * *
KP.2 1589 7 8.894691 6.243829 -4.487657 0.058426 *
XEC.29 135 4 8.457912 8.457912 -8.915824 0.535261 * *
BA.5.1.17 357 3 8.456578 -1.543422 11.086845 0.000024 * *
JN.1.29 69 4 7.971640 7.971640 -7.943281 0.327915 * *
MC.8 93 4 7.731975 7.731975 -7.463950 0.257947 * *
XEC.39 155 4 7.208205 7.208205 -6.416409 0.153355 * *
MC.1 932 7 7.060566 6.073660 -4.147321 0.049292 *
KP.3.1.4 511 7 6.889559 5.992689 -3.985378 0.045502 *
MC.9 298 4 6.547233 6.547233 -5.094467 0.078866 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 21 254.192233 NaN NaN NaN * * *
LF.7 58 21 252.885348 208.888377 -61.776754 3.543696e-02 * *
XFG.2 500 21 244.896342 199.918994 -43.837988 4.506454e-06 *
XFG.3.1 87 21 238.660957 189.640359 -23.280718 1.546278e-10 *
XFG.1 14 21 223.954846 173.714357 8.571285 1.875634e-17 *
LF.7.1 165 21 185.740514 131.200980 93.598040 6.443445e-36 *
LF.7.7.1 188 21 181.963602 113.341668 129.316665 1.128804e-43 *
LF.7.1.8 44 21 177.680110 112.172322 131.655356 3.503436e-44 *
LF.7.6 15 21 168.704612 108.924182 138.151636 1.365239e-45 *
LF.7.1.2 26 21 167.580693 102.040983 151.918034 1.396661e-48 *



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3326_C|A, 3431_G|T, 3565_T|C, 3917_A|G, 3951_3953, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 6268_C|T,
6741_G|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T,
12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16173_C|T, 16600_T|C, 17410_C|T, 18048_T|C, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28473_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29367_C|T,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/CA-LACPHL-AY13158/2025


Target: 530 samples Number of changes: 154
BC: JN.11 + XFG.2 BC BR: 4-5 BC BR coord: 2067 - 2068
Direction L1: << Initial region span: 1-4,5-154Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.04e-238Rec. model vs L2: 8.32e-17
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -2.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -2.470933 0.618783 * *
PD.2 21 4 7.675851 1.065842 11.868317 0.000476 * *
KP.4.2.4 22 4 7.629331 -0.408730 14.817461 0.000109 * *
KR.1.4 24 4 7.408788 0.164265 13.671469 0.000194 * *
KP.3.1.2 28 4 7.277693 7.277693 -0.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -0.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -0.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 0.546188 12.907624 0.000283 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 5 294.433454 NaN NaN NaN * * *
XFG.3 480 6 287.866398 277.866398 -211.732796 6.364150e-08 *
LF.7 58 6 286.350487 276.350487 -208.700975 1.398892e-08 *
XFG.3.1 87 6 267.087493 257.087493 -170.174985 6.013137e-17 *
XFG.1 14 6 237.190678 227.190678 -110.381355 6.249821e-30 *
LF.7.1 165 12 195.285288 184.660805 -25.321609 2.115063e-48
LF.7.7.1 188 12 186.607347 178.530009 -13.060018 4.603605e-51
LF.7.3 54 12 183.675368 172.993384 -1.986767 1.816679e-53
LF.7.1.8 44 12 174.724215 164.118082 15.763837 2.540473e-57
LF.7.6 15 12 173.630791 163.024657 17.950687 8.498889e-58



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10570_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13378_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 18981_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21127_A|G, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28695_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/CT-DPH-1292714001/2025


Target: 530 samples Number of changes: 150
BC: LF.7 + BE.5 BC BR: 147-148 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-142,148-150Gap history (edge excluded): 142-148
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.88e-07 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 142 309.587062 NaN NaN NaN * * *
XFG.3 480 148 308.417909 302.391709 -270.783418 8.543495e-02 *
XFG.2 500 142 300.663746 295.926543 -257.853086 1.330215e-04 * *
XFG.3.1 87 148 275.208799 269.182598 -204.365197 3.242555e-16
XFG.1 14 148 259.534111 253.507911 -173.015822 5.050348e-23
LF.7.1.8 44 142 224.571938 219.834735 -105.669470 1.197994e-37 *
LF.7.1 165 142 219.939926 215.184485 -96.368970 1.145474e-39 *
LF.7.6 15 142 216.244100 211.506897 -89.013794 2.889226e-41 *
LF.7.7.1 188 142 214.706097 209.968894 -85.937788 6.225003e-42 *
LF.7.3 54 142 206.001218 201.264015 -68.528030 1.031825e-45 *
|||||

BE.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BE.5 231 148 7.835908 NaN NaN NaN * * *
JN.1.13.1 751 144 7.032025 1.769229 4.461543 0.002323 *
KP.1.1.3 979 144 6.892653 1.632922 4.734156 0.002029 *
JN.1.2 650 144 6.563489 1.305311 5.389378 0.001459 *
LB.1.3 778 144 6.281969 1.023032 5.953935 0.001103 *
LP.8.1.1 2345 144 4.777156 -0.485641 8.971282 0.000244 *
JN.1 17255 144 4.055319 -1.206550 10.413101 0.000119 *
KP.3.1.1 12013 144 3.973361 -1.289186 10.578372 0.000109 *
JN.1.4 8971 144 3.963317 -1.296691 10.593382 0.000108 *
XFG.3.1 87 144 2.365293 -2.897503 13.795007 0.000022 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12238_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 20270_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25605_A|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29482_C|T, 29510_A|C

Case 58 (XFG): USA/CT-DPH-1302633001/2025


Target: 530 samples Number of changes: 154
BC: KP.3.1.1 + LF.7 BC BR: 12-13 BC BR coord: 4068 - 4069
Direction L1: << Initial region span: 1-10,13-154Gap history (edge excluded): 10-13
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.39e-135Rec. model vs L2: 2.90e-27
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 10 13.891039 NaN NaN NaN * * *
KS.1.1.2 252 5 9.308002 -12.386685 54.773370 1.621637e-11
LB.1.3.1 292 5 7.915789 -13.784194 57.568387 3.998907e-12
KP.1.1.1 578 5 7.234155 -14.492697 58.985394 1.966040e-12
BA.2.86.1 1343 5 7.187877 -16.878703 63.757406 1.810506e-13
MC.11.2 146 3 6.967997 -21.114995 72.229989 2.621578e-15
BA.2.47 679 3 6.006357 -58.208586 146.417172 2.034272e-31
BN.1.5 1025 4 5.606905 -63.827622 157.655244 7.373505e-34
MU.2.1.1 10 3 5.379225 -22.676131 75.352263 5.508881e-16
MC.17 46 3 5.239463 -22.815893 75.631787 4.789191e-16
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 13 308.827859 NaN NaN NaN * * *
XFG.2 500 12 306.418196 303.455925 -278.911850 4.630919e-03 * *
XFG.3 480 13 295.388436 295.388436 -262.776873 1.455734e-06 *
XFG.3.1 87 13 263.410830 263.410830 -198.821659 1.880809e-20 *
XFG.1 14 13 246.254438 246.254438 -164.508877 6.668418e-28 *
LF.7.1.8 44 24 231.469563 210.831531 -93.663062 2.748785e-43
LF.7.1 165 24 224.240243 203.642615 -79.285231 2.083219e-46
LF.7.7.1 188 38 219.628151 200.063133 -72.126265 5.807118e-48
LF.7.6 15 15 204.686595 195.763172 -63.526344 7.879423e-50
LF.7.1.2 26 24 195.403566 174.812055 -21.624110 6.249619e-59



Target sequence

, 186_C|T, 241_C|T, 670_T|G, 813_C|T, 897_C|A, 1177_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4002_C|T, 4068_C|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6543_C|T, 7842_A|G,
7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12676_C|T,
12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T,
29510_A|C

Case 58 (XFG): USA/CT-DPH-1304113001/2025


Target: 530 samples Number of changes: 152
BC: XEC.29 + XFG.3 BC BR: 5-6 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-5,9-152Gap history (edge excluded): 5-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.99e-220Rec. model vs L2: 3.46e-14
Flags: Model_2BP_Bad_L1_opp

XEC.29 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.29 135 5 10.664726 NaN NaN NaN * * *
MC.9 298 5 7.269081 7.269081 -4.538162 3.354055e-02 * *
KP.2 1589 5 7.083669 7.083669 -4.167338 2.787570e-02 * *
KP.3.1.4 511 5 6.175261 6.175261 -2.350521 1.122064e-02 * *
MC.1 932 5 5.655268 5.655268 -1.310537 6.670903e-03 * *
KP.2.2 1334 5 4.924695 4.924695 0.150609 3.214768e-03 * *
JN.1.39 1007 5 4.819029 4.819029 0.361941 2.894335e-03 * *
LB.1 1128 5 4.587727 4.587727 0.824545 2.299646e-03 * *
BF.14 1581 4 4.370988 -5.629012 21.258023 8.378599e-08 *
KP.3.1.1 12013 6 4.091904 3.744455 2.511091 9.878299e-04 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 323.955272 NaN NaN NaN * * *
LF.7 58 9 309.956453 279.956453 -215.912907 8.315287e-07 *
XFG.2 500 8 298.714244 281.013151 -218.026302 2.400100e-06 *
XFG.3.1 87 9 291.566276 261.566276 -179.132551 8.574360e-15 *
XFG.1 14 9 274.571728 244.571728 -145.143455 3.567525e-22 *
LF.7.7.1 188 17 237.921608 189.544250 -35.088501 4.521819e-46
LF.7.1 165 17 230.871754 202.263752 -60.527503 1.511955e-40
LF.7.1.8 44 17 222.705226 183.169373 -22.338746 7.703460e-49
LF.7.6 15 17 219.416831 179.880978 -15.761956 2.869835e-50
LF.7.3 54 17 215.969767 176.358064 -8.716127 8.494550e-52



Target sequence

, 66_C|T, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1213_C|T, 1288_C|T, 2086_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G,
7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25606_G|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/CT-USAFSAM-S23777/2025


Target: 530 samples Number of changes: 152
BC: JN.11 + XFG.2 BC BR: 4-5 BC BR coord: 2067 - 2068
Direction L1: << Initial region span: 1-4,6-152Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.03e-229Rec. model vs L2: 8.32e-17
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -2.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -2.470933 0.618783 * *
PD.2 21 4 7.675851 1.065842 11.868317 0.000476 * *
KP.4.2.4 22 4 7.629331 -0.408730 14.817461 0.000109 * *
KR.1.4 24 4 7.408788 0.164265 13.671469 0.000194 * *
KP.3.1.2 28 4 7.277693 7.277693 -0.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -0.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -0.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 0.546188 12.907624 0.000283 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 6 309.396975 NaN NaN NaN * * *
XFG.3 480 7 303.171216 283.171216 -226.342433 1.828390e-11 *
LF.7 58 7 302.503793 282.503793 -225.007587 9.402928e-12 *
XFG.3.1 87 7 269.640359 249.640359 -159.280718 5.013892e-26 *
XFG.1 14 7 253.714357 233.714357 -127.428715 6.081845e-33 *
LF.7.7.1 188 13 213.692328 205.090802 -70.181604 2.250898e-45
LF.7.1 165 13 211.503267 190.878784 -41.757568 1.517159e-51
LF.7.1.8 44 13 204.724215 184.118082 -28.236163 1.758735e-54
LF.7.1.2 26 13 195.612259 174.927683 -9.855367 1.794875e-58
LF.7.6 15 13 189.530316 168.924182 2.151636 4.426861e-61



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21846_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23592_A|C, 23599_T|G, 23604_C|G, 23635_C|T, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MA-MASPHL-14177/2025


Target: 530 samples Number of changes: 156
BC: XFG.3 + KP.3.1.5 + XFG.3BC BR: 5-6, 9-10 BC BR coord: 896 - 897, 3430 - 3431
Direction L1: << Initial region span: 1-5,7-9,10-156Gap history (edge excluded): 5-10 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.86e-02
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 1.44e-217
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 5 9.640979 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 7 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 7 7.613984 -2.386016 22.772033 1.000000e+00 * *
NL.11 57 7 7.208518 -2.791482 23.582963 6.669768e-01 * *
XBB.4 49 6 6.609415 6.609415 4.781171 8.062670e+03 * *
B.1.1.304 143 8 6.536776 -19.539319 57.078638 3.545505e-08 *
AZ.5 21 8 6.536776 -23.368480 64.736960 7.697156e-10 *
B.1.1.434 1274 8 6.534418 -27.588067 73.176135 1.131378e-11 *
XBB.1.5.92 41 6 6.272764 6.272764 5.454472 5.767535e+03 * *
JE.1.1.1 46 7 5.577102 -11.675249 41.350497 9.234306e-05 * *
LE.1.2 19 7 5.362692 -12.680191 43.360383 3.380168e-05 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 10 279.842351 NaN NaN NaN * * *
LF.7 58 10 269.362742 279.250049 -204.500098 3.589186e-05 * *
XFG.2 500 10 251.669760 259.218842 -164.437684 7.179224e-14 *
XFG.3.1 87 10 239.813677 248.482412 -142.964825 1.555087e-18 *
XFG.1 14 10 218.661809 226.646956 -99.293912 5.116050e-28 *
LF.7.1 165 18 186.187225 188.465008 -22.930015 1.341441e-44
LF.7.1.2 26 18 181.834837 183.570539 -13.141078 1.003922e-46
LF.7.7.1 188 14 180.598486 177.956410 -1.912821 3.657097e-49
LF.7.1.8 44 18 177.515938 178.161865 -2.323731 4.489178e-49
LF.7.1.5 40 18 156.918808 157.072878 39.854244 3.126566e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18129_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MD-MDH-11764/2025


Target: 530 samples Number of changes: 146
BC: LF.1 + LF.7 BC BR: 5-6 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-5,9-146Gap history (edge excluded): 5-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.10e-138Rec. model vs L2: 1.23e-07
Flags: Model_2BP_Bad_L1_opp

LF.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.1 141 5 12.979047 NaN NaN NaN * * *
MC.6 366 5 11.261938 11.261938 -8.523876 1.790661e-01 * *
MC.10.1 650 5 9.038076 9.038076 -4.076152 1.944821e-02 * *
JN.1.4.4 32 4 8.345935 6.143533 1.712934 1.075467e-03 * *
BF.40 56 4 8.145755 -1.854245 17.708490 3.607791e-07 *
FL.5.1 10 4 6.948982 -3.051018 20.102037 1.092093e-07 *
BQ.1.1.41 818 4 6.470822 -3.529178 21.058357 6.757687e-08 *
GS.1 109 4 5.997751 -4.002249 22.004497 4.223570e-08 *
BE.1.2 467 4 5.878484 -4.121516 22.243032 3.745971e-08 *
BQ.1.1.4 2753 4 5.833933 -4.166067 22.332134 3.581138e-08 *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 9 252.204253 NaN NaN NaN * * *
XFG.3 480 9 242.615949 221.553098 -93.106196 6.806823e-05 * *
XFG.2 500 9 225.532594 196.930693 -43.861386 1.375444e-15 *
XFG.1 14 9 216.855594 195.782273 -41.564545 4.355161e-16 *
XFG.3.1 87 9 209.047999 187.974677 -25.949355 1.775562e-19 *
LF.7.1.8 44 17 188.979180 161.316976 27.366048 4.688618e-31
LF.7.7.1 188 13 166.904493 135.307771 79.384457 2.383509e-42
LF.7.1.2 26 17 165.871947 138.256263 73.487475 4.531209e-41
LF.7.1.5 40 17 160.276110 132.660426 84.679149 1.683978e-43
LF.7.1 165 17 158.101789 130.461639 89.076722 1.865901e-44



Target sequence

, 44_C|T, 241_C|T, 481_A|G, 670_T|G, 897_C|A, 2485_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23148_A|C, 23222_G|A, 23271_C|T,
23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T,
28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MI-UM-10064755202/2025


Target: 530 samples Number of changes: 153
BC: XFG.3 + NY.15 + XFG.3 BC BR: 134-135, 146-147 BC BR coord: 26872 - 26873, 28880 - 28881
Direction L1: >> Initial region span: 1-134,136-146,147-153Gap history (edge excluded): 134-147 -> 134-136
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.26e-01
Rec. model vs L1: 3.43e-22Rec. model vs L2: 1.17e-180
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 134 287.998031 NaN NaN NaN * * *
LF.7 58 139 281.013438 284.704425 -247.408850 4.882614e-08
XFG.2 500 134 264.611688 278.175804 -234.351608 7.123762e-11 *
XFG.3.1 87 134 238.035180 250.992096 -179.984191 1.112792e-22 *
XFG.1 14 134 222.185044 235.870198 -149.740397 3.019127e-29 *
LF.7.1.8 44 134 213.864314 211.349996 -100.699992 6.776114e-40 *
LF.7.7.1 188 134 188.199426 192.510309 -63.020618 4.455256e-48 *
LF.7.1 165 134 183.904396 193.083008 -64.166015 7.917571e-48 *
LF.7.6 15 134 180.184030 177.699883 -33.399766 1.648054e-54 *
LF.7.3 54 134 170.077623 167.698837 -13.397673 7.482152e-59 *
|||||

NY.15 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NY.15 216 136 15.911165 NaN NaN NaN * * *
KP.3.1.11 31 141 12.700518 -1.884552 27.769104 4.117888e-04 *
MD.1.1 24 141 12.312095 -2.272976 28.545951 2.788044e-04 *
LF.9 48 141 10.653867 -3.931204 31.862407 5.327731e-05 *
JN.1.16.3 52 141 10.573824 -4.030664 32.061329 4.820730e-05 *
JN.1.4 8971 136 10.231699 9.001183 5.997634 2.197708e+01 * *
CM.8.1 200 135 10.147548 10.147548 3.704904 6.940785e+01 * *
CM.4 76 143 10.147058 -13.794824 51.589649 2.768390e-09
CM.8.1.4 19 143 10.147058 -13.954338 51.908676 2.359066e-09
CM.6.1 14 143 10.147058 -13.674353 51.348706 3.121351e-09
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 147 13.542054 None None None * * *



Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9079_A|G, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21483_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27059_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27577_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28550_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MI-UM-10064755202/2025


Target: 530 samples Number of changes: 153
BC: XFG.3 + NY.15 + XFG.3 BC BR: 134-135, 146-147 BC BR coord: 26872 - 26873, 28880 - 28881
Direction L1: >> Initial region span: 1-134,136-146,147-153Gap history (edge excluded): 134-147 -> 134-136
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.26e-01
Rec. model vs L1: 3.43e-22Rec. model vs L2: 1.17e-180
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 134 287.998031 NaN NaN NaN * * *
LF.7 58 139 281.013438 284.704425 -247.408850 4.882614e-08
XFG.2 500 134 264.611688 278.175804 -234.351608 7.123762e-11 *
XFG.3.1 87 134 238.035180 250.992096 -179.984191 1.112792e-22 *
XFG.1 14 134 222.185044 235.870198 -149.740397 3.019127e-29 *
LF.7.1.8 44 134 213.864314 211.349996 -100.699992 6.776114e-40 *
LF.7.7.1 188 134 188.199426 192.510309 -63.020618 4.455256e-48 *
LF.7.1 165 134 183.904396 193.083008 -64.166015 7.917571e-48 *
LF.7.6 15 134 180.184030 177.699883 -33.399766 1.648054e-54 *
LF.7.3 54 134 170.077623 167.698837 -13.397673 7.482152e-59 *
|||||

NY.15 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NY.15 216 136 15.911165 NaN NaN NaN * * *
KP.3.1.11 31 141 12.700518 -1.884552 27.769104 4.117888e-04 *
MD.1.1 24 141 12.312095 -2.272976 28.545951 2.788044e-04 *
LF.9 48 141 10.653867 -3.931204 31.862407 5.327731e-05 *
JN.1.16.3 52 141 10.573824 -4.030664 32.061329 4.820730e-05 *
JN.1.4 8971 136 10.231699 9.001183 5.997634 2.197708e+01 * *
CM.8.1 200 135 10.147548 10.147548 3.704904 6.940785e+01 * *
CM.4 76 143 10.147058 -13.794824 51.589649 2.768390e-09
CM.8.1.4 19 143 10.147058 -13.954338 51.908676 2.359066e-09
CM.6.1 14 143 10.147058 -13.674353 51.348706 3.121351e-09
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 147 13.542054 None None None * * *



Target sequence

, 241_C|T, 509_523, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9079_A|G, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21483_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27059_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27577_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28550_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MN-MDH-47445/2025


Target: 530 samples Number of changes: 153
BC: MC.33 + XFG.3 BC BR: 5-6 BC BR coord: 1426 - 1427
Direction L1: << Initial region span: 1-5,6-153Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.62e-01
Rec. model vs L1: 2.16e-233Rec. model vs L2: 1.37e-15
Flags: Model_1BP_Best

MC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.33 31 5 12.303173 NaN NaN NaN * * *
KP.4.1.1 12 4 9.895496 -0.104504 10.209008 4.077608e-06 *
NY.12 62 4 9.335620 -0.664380 11.328760 2.329167e-06 *
JN.13 15 4 9.161527 -0.838473 11.676947 1.955235e-06 *
LF.7.1 165 5 7.947883 7.947883 -5.895765 1.284244e-02 * *
MD.1 19 4 7.826526 -2.173474 14.346949 5.145362e-07 *
KP.2.3.13 25 4 7.552089 -2.447911 14.895822 3.908273e-07 *
MC.29 54 4 7.475128 -2.524872 15.049744 3.625875e-07 *
XFJ.1 59 4 7.334994 -2.665006 15.330012 3.152184e-07 *
KP.3.2 737 5 7.309689 7.309689 -4.619377 6.771721e-03 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 320.978235 NaN NaN NaN * * *
XFG.2 500 6 312.095267 304.556637 -269.113274 7.357210e-08 *
LF.7 58 6 295.993193 295.993193 -251.986386 1.409783e-11 *
XFG.3.1 87 6 262.157898 262.157898 -184.315796 2.849696e-26 *
XFG.1 14 6 247.211449 247.211449 -154.422899 9.164232e-33 *
LF.7.1 165 1 212.378145 204.430262 -68.860524 2.415339e-51
LF.7.1.8 44 16 202.916100 197.408311 -54.816622 2.158892e-54
LF.7.7.1 188 12 196.168587 186.726282 -33.452563 4.940767e-59
LF.7.6 15 12 182.840632 182.234498 -24.468997 5.543858e-61
LF.7.1.2 26 16 181.151893 175.612183 -11.224366 7.355482e-64



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1288_C|T, 1426_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6541_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19217_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28281_A|G, 28297_T|C, 28311_C|T, 28362_28370, 28528_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MN-MDH-47488/2025


Target: 530 samples Number of changes: 153
BC: KP.4.1.1 + XFG.2 BC BR: 6-7 BC BR coord: 3037 - 3038
Direction L1: << Initial region span: 1-6,8-153Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.16e-01
Rec. model vs L1: 1.54e-218Rec. model vs L2: 2.58e-11
Flags: Model_1BP_Best

KP.4.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.4.1.1 12 6 10.976590 NaN NaN NaN * * *
JN.13 15 6 10.242621 10.242621 -6.485242 0.481909 * *
JN.1.46 308 7 9.884875 7.197732 -0.395465 0.022937 * *
MC.33 31 6 9.804366 9.804366 -5.608732 0.310367 * *
NY.12 62 4 9.335620 4.042019 5.915962 0.000973 *
MD.1 19 6 8.907620 8.907620 -3.815240 0.126818 * *
JN.18 316 7 8.745078 6.083578 1.832845 0.007521 * *
KP.2.3.13 25 6 8.633183 8.633183 -3.266366 0.096328 * *
MC.24 831 7 8.586741 6.892128 0.215744 0.016823 * *
XFJ.1 59 6 8.416088 8.416088 -2.832176 0.077305 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 8 311.024223 NaN NaN NaN * * *
XFG.3 480 8 306.810313 296.810313 -257.620627 1.477232e-02 * *
LF.7 58 8 294.929491 284.929491 -233.858981 1.023364e-07 *
XFG.3.1 87 17 261.178496 251.076804 -166.153608 2.027639e-22
XFG.1 14 17 247.451939 236.130355 -136.260711 6.553293e-29
LF.7.1 165 17 219.915996 193.349168 -50.698336 1.727196e-47
LF.7.1.8 44 17 212.916100 186.327217 -36.654434 1.536112e-50
LF.7.7.1 188 17 205.348216 175.645188 -15.290375 3.533116e-55
LF.7.6 15 17 192.014928 171.153404 -6.306808 3.964383e-57
LF.7.1.2 26 17 191.151893 164.570310 6.859381 5.474525e-60



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3092_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5037_G|A, 5239_C|T, 6183_A|G, 6541_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17825_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24902_A|G, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28281_A|G, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MN-MDH-47506/2025


Target: 530 samples Number of changes: 150
BC: JN.11 + LF.7 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-150Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.94e-228Rec. model vs L2: 4.16e-08
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -8.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -8.470933 0.618783 * *
PD.2 21 4 7.675851 7.675851 -7.351701 0.353455 * *
KP.4.2.4 22 4 7.629331 7.629331 -7.258661 0.337902 * *
KR.1.4 24 4 7.408788 7.408788 -6.817576 0.271173 * *
KP.3.1.2 28 4 7.277693 7.277693 -6.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -6.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -6.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 7.156197 -6.312394 0.210136 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 6 325.993193 NaN NaN NaN * * *
XFG.3 480 6 325.966793 315.966793 -293.933586 9.704455e-01 * *
XFG.2 500 5 321.585552 314.046922 -290.093844 1.422741e-01 * *
XFG.3.1 87 6 292.157898 282.157898 -226.315796 2.021372e-15 *
XFG.1 14 6 277.211449 267.211449 -196.422899 6.500454e-22 *
LF.7.1 165 12 235.054745 224.430262 -110.860524 1.713270e-40
LF.7.1.8 44 12 228.014445 217.408311 -96.816622 1.531364e-43
LF.7.7.1 188 12 226.168587 218.091249 -98.182497 3.022726e-43
LF.7.6 15 12 212.840632 202.234498 -66.468997 3.932419e-50
LF.7.3 54 12 209.604289 198.922305 -59.844610 1.428807e-51



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18636_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/MN-MDH-47532/2025


Target: 530 samples Number of changes: 154
BC: LF.7.7.1 + XFG.2 BC BR: 10-11 BC BR coord: 3566 - 3567
Direction L1: << Initial region span: 1-10,12-154Gap history (edge excluded): 10-12
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.77e-63 Rec. model vs L2: 3.13e-16
Flags: Model_2BP_Bad_L1_opp

LF.7.7.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.7.1 188 10 14.577215 NaN NaN NaN * * *
LB.1.3.1 292 10 14.371388 14.371388 -8.742775 0.814647 * *
LB.1.3 778 10 12.936862 12.936862 -5.873723 0.193980 * *
KP.3.1.1 12013 10 12.053449 12.053449 -4.106898 0.080460 * *
KP.2.2 1334 10 11.322836 11.322836 -2.645672 0.038774 * *
KP.1.1.1 578 10 11.188305 11.188305 -2.376610 0.033878 * *
XEC.2 921 10 10.708486 10.708486 -1.416972 0.020963 * *
LB.1.7 1971 10 10.525027 10.525027 -1.050055 0.017422 * *
KP.1.1.3 979 10 10.313570 10.313570 -0.627140 0.014122 * *
JN.1 17255 10 10.293289 10.293289 -0.586578 0.013843 * *
|||||

XFG.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 12 306.368618 NaN NaN NaN * * *
LF.7 58 12 297.746406 287.746406 -243.492811 1.795602e-04 * *
XFG.3 480 12 297.741957 287.741957 -243.483913 1.786646e-04 * *
XFG.3.1 87 12 264.002452 254.002452 -176.004904 3.971392e-19 *
XFG.1 14 12 248.894160 238.894160 -145.788321 1.093767e-25 *
LF.7.1 165 14 215.054745 196.131322 -60.262644 2.926315e-44
LF.7.1.8 44 14 208.014445 189.091022 -46.182044 2.563823e-47
LF.7.7.1 188 14 206.168587 178.414326 -24.828652 5.926447e-52
LF.7.6 15 14 192.840632 173.917209 -15.834418 6.583688e-54
LF.7.3 54 14 189.604289 170.662174 -9.324348 2.540041e-55



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3931_T|A, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11541_T|G, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16323_C|T, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT,
21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25520_T|C, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/MN-MDH-47545/2025


Target: 530 samples Number of changes: 152
BC: XFG.3 + PQ.5 BC BR: 145-146 BC BR coord: 28361 - 28362
Direction L1: >> Initial region span: 1-145,146-152Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.24e-35 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 145 287.019003 NaN NaN NaN * * *
XFG.2 500 145 283.539487 283.539487 -237.078974 3.080741e-02 * *
LF.7 58 145 279.587062 279.587062 -229.174125 5.902290e-04 * *
XFG.3.1 87 145 243.919801 243.919801 -157.839603 1.913850e-19 *
XFG.1 14 145 228.245114 228.245114 -126.490229 2.980862e-26 *
LF.7.1.8 44 145 208.605626 208.605626 -87.211252 8.806396e-35 *
LF.7.6 15 145 200.443583 200.443583 -70.887166 2.517417e-38 *
LF.7.1 165 145 189.939926 189.939926 -49.879851 6.897500e-43 *
LF.7.7.1 188 145 184.706097 184.706097 -39.412194 3.674177e-45 *
LF.7.3 54 145 176.001218 176.001218 -22.002436 6.090131e-49 *
|||||

PQ.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
PQ.5 11 146 16.976002 NaN NaN NaN * * *
PQ.14 26 146 16.936781 16.936781 -19.873562 9.607894e-01 * *
PQ.12 17 146 16.915377 16.915377 -19.830754 9.417645e-01 * *
PQ.10 24 146 16.888990 16.888990 -19.777980 9.185123e-01 * *
PQ.1 52 146 16.773809 16.773809 -19.547619 8.187308e-01 * *
NB.1.8.1 357 146 16.760158 16.760158 -19.520315 8.065414e-01 * *
PQ.2 91 146 16.746984 16.746984 -19.493968 7.945336e-01 * *
PQ.8 13 146 16.728905 16.728905 -19.457810 7.827045e-01 * *
PQ.4 29 146 16.635001 16.635001 -19.270001 7.117703e-01 * *
DV.7.1.1 23 147 8.685330 -1.314670 16.629341 1.139604e-08 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4714_T|C, 5239_C|T, 6183_A|G, 6543_C|T, 7842_A|G, 7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 14781_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23593_G|C, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28432_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 29164_T|C, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NJ-GBW-GKISBBBH44036/2025


Target: 530 samples Number of changes: 151
BC: XFG.3 + HV.1.11 + XFG.3BC BR: 6-7, 8-9 BC BR coord: 896 - 897, 2789 - 2790
Direction L1: << Initial region span: 1-6,7-8,9-151Gap history (edge excluded): 6-9 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.47e-10
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 9.468747 None None None * * *
|||||

HV.1.11 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
HV.1.11 24 7 8.135609 NaN NaN NaN * * *
HK.1 30 7 7.219319 7.219319 -6.438637 4.005166e-01 * *
HV.1.1 536 7 6.732410 6.732410 -5.464820 2.453671e-01 * *
EG.5.1.16 519 7 5.976122 5.976122 -3.952243 1.153251e-01 * *
B.1.1.428 42 8 5.908262 -10.951078 29.902156 5.146237e-09 *
A.27 515 8 5.908262 -12.451723 32.903445 1.148281e-09 *
AY.71 260 8 5.908262 -4.091738 16.183477 4.906253e-06 *
AY.72 300 8 5.908262 -4.091738 16.183477 4.906253e-06 *
AY.73 462 8 5.908262 -4.091738 16.183477 4.906253e-06 *
B.1.1.181 17 8 5.908262 -4.091738 16.183477 4.906253e-06 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 315.994603 NaN NaN NaN * * *
LF.7 58 9 315.327180 315.214487 -286.428974 3.535750e-05 * *
XFG.2 500 8 312.290173 309.452453 -274.904907 1.108597e-07 *
XFG.3.1 87 9 282.463746 281.132481 -218.264963 5.566140e-20 *
XFG.1 14 9 266.537744 264.522890 -185.045781 3.420537e-27 *
LF.7.1 165 15 224.326654 234.135537 -124.271074 2.167130e-40
LF.7.1.8 44 15 217.547602 214.176278 -84.352557 4.649081e-49
LF.7.7.1 188 1 215.652269 214.811489 -85.622979 8.772919e-49
LF.7.6 15 15 202.353703 200.916485 -57.832971 8.102560e-55
LF.7.3 54 15 199.011999 196.199305 -48.398611 7.259786e-57



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NJ-GBW-GKPLAAAA70247/2025


Target: 530 samples Number of changes: 152
BC: XFG.3 + HV.1.11 + XFG.3BC BR: 6-7, 8-9 BC BR coord: 896 - 897, 2789 - 2790
Direction L1: << Initial region span: 1-6,7-8,9-152Gap history (edge excluded): 6-9 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.47e-10
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 9.468747 None None None * * *
|||||

HV.1.11 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
HV.1.11 24 7 8.135609 NaN NaN NaN * * *
HK.1 30 7 7.219319 7.219319 -6.438637 4.005166e-01 * *
HV.1.1 536 7 6.732410 6.732410 -5.464820 2.453671e-01 * *
EG.5.1.16 519 7 5.976122 5.976122 -3.952243 1.153251e-01 * *
B.1.1.428 42 8 5.908262 -10.951078 29.902156 5.146237e-09 *
A.27 515 8 5.908262 -12.451723 32.903445 1.148281e-09 *
AY.71 260 8 5.908262 -4.091738 16.183477 4.906253e-06 *
AY.72 300 8 5.908262 -4.091738 16.183477 4.906253e-06 *
AY.73 462 8 5.908262 -4.091738 16.183477 4.906253e-06 *
B.1.1.181 17 8 5.908262 -4.091738 16.183477 4.906253e-06 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 320.273315 NaN NaN NaN * * *
LF.7 58 9 320.178790 320.066097 -294.132194 6.283489e-05 * *
XFG.2 500 8 314.987618 312.149898 -278.299797 2.294880e-08 *
XFG.3.1 87 9 285.811278 284.480014 -222.960028 2.207149e-20 *
XFG.1 14 9 256.537744 254.522890 -163.045781 2.160432e-33 *
LF.7.1 165 15 228.643587 238.452470 -130.904940 2.255572e-40
LF.7.7.1 188 1 220.021027 219.180248 -92.360495 9.647218e-49
LF.7.1.8 44 15 207.547602 204.176278 -62.352557 2.936388e-55
LF.7.1.2 26 15 201.202901 198.835611 -51.671222 1.408254e-57
PC.3 42 15 199.379236 196.551829 -47.103658 1.433237e-58



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 13427_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NJ-PHEL-V25011860/2025


Target: 530 samples Number of changes: 150
BC: JN.1.53.1 + LF.7 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-150Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.44e-201Rec. model vs L2: 6.10e-09
Flags: Model_2BP_Bad_L1_opp

JN.1.53.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.53.1 12 4 10.761787 NaN NaN NaN * * *
JN.4 91 4 9.333671 9.333671 -10.667342 0.240508 * *
NL.18 10 4 8.546213 8.546213 -9.092426 0.109154 * *
XEC.17 13 4 8.283849 8.283849 -8.567698 0.084163 * *
LD.2 13 4 8.283849 8.283849 -8.567698 0.084163 * *
JN.1.1.10 17 4 8.015585 8.015585 -8.031170 0.064248 * *
JN.1.64.1 14 4 7.901440 7.901440 -7.802879 0.057269 * *
MC.10.1.5 19 4 7.850292 7.850292 -7.700584 0.054476 * *
JN.1.7.2 180 5 7.462227 5.610990 -3.221981 0.005799 * *
XEC.2 921 5 7.340305 3.986077 0.027846 0.001142 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 6 346.907477 NaN NaN NaN * * *
XFG.3 480 1 320.935805 315.176827 -290.353655 3.654104e-10
XFG.2 500 6 308.801106 291.262476 -242.524952 1.501856e-20 *
XFG.3.1 87 3 288.165668 283.451414 -226.902828 6.092401e-24
XFG.1 14 6 264.571728 254.571728 -169.143455 1.747285e-36 *
LF.7.1 165 16 227.427289 211.941555 -83.883111 5.350447e-55
LF.7.1.8 44 16 220.622921 205.115133 -70.230265 5.812062e-58
LF.7.7.1 188 12 218.986556 199.544250 -59.088501 2.214675e-60
LF.7.1.2 26 16 213.318683 197.778973 -55.557947 3.791231e-61
LF.7.6 15 12 200.487112 189.880978 -39.761956 1.405574e-64



Target sequence

, 241_C|T, 583_C|T, 670_T|G, 897_C|A, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6673_T|C, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22883_C|A,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24034_C|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/NJ-PHEL-V25012011/2025


Target: 530 samples Number of changes: 150
BC: JN.1.7.8 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,5-150Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.80e-210Rec. model vs L2: 1.27e-14
Flags: Model_2BP_Bad_L1_opp

JN.1.7.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.7.8 34 4 10.445059 NaN NaN NaN * * *
JN.1.11 43 4 9.890658 9.890658 -9.781316 5.740723e-01 * *
MC.37 21 3 8.888229 -4.739126 19.478252 2.542367e-07 *
KP.2.3.3 149 4 7.472009 7.472009 -4.944018 5.104743e-02 * *
LA.1 149 4 7.449603 7.449603 -4.899205 5.003663e-02 * *
JN.1.16.1 466 4 5.159737 5.159737 -0.319475 5.067032e-03 * *
KP.3.2 737 4 4.943160 4.943160 0.113679 4.086771e-03 * *
MC.10.1 650 4 4.484871 4.484871 1.030257 2.579912e-03 * *
BA.5.2.23 644 3 4.295678 -5.704322 21.408643 9.685992e-08 *
LB.1.3 778 4 4.119803 4.119803 1.760394 1.790966e-03 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 5 303.613273 NaN NaN NaN * * *
LF.7 58 5 303.571870 303.571870 -267.143740 9.559975e-01 * *
XFG.2 500 5 298.801106 291.262476 -242.524952 4.308159e-06 *
XFG.3.1 87 5 282.540815 282.540815 -225.081629 7.034671e-10 *
XFG.1 14 5 254.571728 254.571728 -169.143455 5.012185e-22 *
LF.7.1.8 44 11 219.754954 219.148820 -98.297641 2.076427e-37
LF.7.1 165 11 212.566038 211.941555 -83.883111 1.534806e-40
LF.7.7.1 188 11 208.986556 199.544250 -59.088501 6.352918e-46
LF.7.6 15 11 190.487112 189.880978 -39.761956 4.031968e-50
LF.7.3 54 11 187.040048 186.358064 -32.716127 1.193440e-51



Target sequence

, 241_C|T, 670_T|G, 896_G|A, 897_C|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17550_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19648_G|T, 19955_C|T, 20055_A|G, 20178_C|T, 20670_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/NJ-PHEL-V25012357/2025


Target: 530 samples Number of changes: 151
BC: JN.4 + LF.7 BC BR: 5-6 BC BR coord: 1514 - 1515
Direction L1: << Initial region span: 1-5,7-151Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.49e-238Rec. model vs L2: 2.40e-15
Flags: Model_2BP_Bad_L1_opp

JN.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.4 91 5 11.875704 NaN NaN NaN * * *
JN.1.53.1 12 4 10.761787 0.761787 10.476426 1.488733e-05 * *
NL.18 10 4 8.546213 -1.453787 14.907574 1.625004e-06 *
LD.2 13 4 8.283849 -8.043214 28.086428 2.232821e-09 *
XEC.17 13 4 8.283849 -1.716151 15.432302 1.252962e-06 *
JN.1.1.10 17 4 8.015585 -1.984415 15.968830 9.564857e-07 *
JN.1.64.1 14 4 7.901440 -2.098560 16.197121 8.525790e-07 *
MC.10.1.5 19 4 7.850292 -2.149708 16.299416 8.109982e-07 *
KP.4.1.2 32 4 7.286775 -2.713225 17.426450 4.609391e-07 *
JN.1.18.5 37 4 7.237880 -2.762120 17.524239 4.406566e-07 *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 7 346.907477 NaN NaN NaN * * *
XFG.3 480 6 315.176827 315.176827 -290.353655 3.654104e-10 *
XFG.2 500 7 308.801106 291.262476 -242.524952 1.501856e-20 *
XFG.3.1 87 6 283.451414 283.451414 -226.902828 6.092401e-24 *
XFG.1 14 7 264.571728 254.571728 -169.143455 1.747285e-36 *
LF.7.1 165 17 227.427289 211.941555 -83.883111 5.350447e-55
LF.7.1.8 44 17 220.622921 205.115133 -70.230265 5.812062e-58
LF.7.7.1 188 13 218.986556 199.544250 -59.088501 2.214675e-60
LF.7.1.2 26 17 213.318683 197.778973 -55.557947 3.791231e-61
LF.7.6 15 13 200.487112 189.880978 -39.761956 1.405574e-64



Target sequence

, 241_C|T, 583_C|T, 670_T|G, 897_C|A, 1514_C|T, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6673_T|C, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22883_C|A, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24034_C|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/NY-PRL-250520_81F07/2025


Target: 530 samples Number of changes: 155
BC: KS.1.3 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,9-155Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.00e-214Rec. model vs L2: 1.13e-08
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1.3 45 4 10.286720 NaN NaN NaN * * *
KP.3.1 1957 8 8.879327 4.771811 -1.543623 0.004026 *
KP.3.2.9 28 4 8.768748 8.768748 -9.537496 0.219808 * *
LK.2.1 10 4 8.699755 8.699755 -9.399510 0.204948 * *
PR.2 20 4 8.648462 8.648462 -9.296923 0.194952 * *
KR.1.1 33 4 8.541924 8.541924 -9.083849 0.174645 * *
JN.2.5 25 4 8.435789 8.435789 -8.871579 0.157237 * *
KP.2.15 253 4 8.319432 8.319432 -8.638864 0.140156 * *
JN.1.16.5 24 4 7.781727 7.781727 -7.563453 0.081676 * *
LF.7.3.1 26 4 7.705023 7.705023 -7.410046 0.075774 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 285.079706 NaN NaN NaN * * *
LF.7 58 9 257.824674 238.888377 -127.776754 5.634715e-17 *
XFG.2 500 9 255.322126 238.966995 -127.933989 6.073570e-17 *
XFG.3.1 87 18 238.660957 219.640359 -89.280718 2.458687e-25
XFG.1 14 18 223.954846 203.714357 -57.428715 2.982384e-32
LF.7.1.8 44 18 204.917733 169.409944 11.180111 3.767830e-47
LF.7.7.1 188 18 203.503019 164.881084 20.237832 4.061976e-49
LF.7.1 165 18 185.740514 150.254780 49.490440 1.807926e-55
LF.7.6 15 18 182.806258 153.025828 43.948344 2.885202e-54
LF.7.3 54 18 178.114496 160.596294 28.807413 5.594812e-51



Target sequence

, 241_C|T, 313_C|T, 670_T|G, 897_C|A, 934_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4584_A|G, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 16376_C|T, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22001_A|G, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/NY-PRL-250520_81F07/2025


Target: 530 samples Number of changes: 155
BC: KS.1.3 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,9-155Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.00e-214Rec. model vs L2: 1.13e-08
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1.3 45 4 10.286720 NaN NaN NaN * * *
KP.3.1 1957 8 8.879327 4.771811 -1.543623 0.004026 *
KP.3.2.9 28 4 8.768748 8.768748 -9.537496 0.219808 * *
LK.2.1 10 4 8.699755 8.699755 -9.399510 0.204948 * *
PR.2 20 4 8.648462 8.648462 -9.296923 0.194952 * *
KR.1.1 33 4 8.541924 8.541924 -9.083849 0.174645 * *
JN.2.5 25 4 8.435789 8.435789 -8.871579 0.157237 * *
KP.2.15 253 4 8.319432 8.319432 -8.638864 0.140156 * *
JN.1.16.5 24 4 7.781727 7.781727 -7.563453 0.081676 * *
LF.7.3.1 26 4 7.705023 7.705023 -7.410046 0.075774 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 285.079706 NaN NaN NaN * * *
LF.7 58 9 257.824674 238.888377 -127.776754 5.634715e-17 *
XFG.2 500 9 255.322126 238.966995 -127.933989 6.073570e-17 *
XFG.3.1 87 18 238.660957 219.640359 -89.280718 2.458687e-25
XFG.1 14 18 223.954846 203.714357 -57.428715 2.982384e-32
LF.7.1.8 44 18 204.917733 169.409944 11.180111 3.767830e-47
LF.7.7.1 188 18 203.503019 164.881084 20.237832 4.061976e-49
LF.7.1 165 18 185.740514 150.254780 49.490440 1.807926e-55
LF.7.6 15 18 182.806258 153.025828 43.948344 2.885202e-54
LF.7.3 54 18 178.114496 160.596294 28.807413 5.594812e-51



Target sequence

, 241_C|T, 313_C|T, 670_T|G, 897_C|A, 934_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4584_A|G, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 16376_C|T, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22001_A|G, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/NY-PRL-250708_81D01/2025


Target: 530 samples Number of changes: 155
BC: XFG.3 + KP.3.1.5 + XFG.3BC BR: 3-4, 7-8 BC BR coord: 896 - 897, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-155Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.82e-02
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 3.08e-218
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 -2.386016 22.772033 1.000000e+00 * *
NL.11 57 5 7.208518 -2.791482 23.582963 6.669768e-01 * *
XBB.4 49 4 6.609415 6.609415 4.781171 8.062670e+03 * *
B.1.1.304 143 6 6.536776 -19.539319 57.078638 3.545505e-08 *
AZ.5 21 6 6.536776 -23.368480 64.736960 7.697156e-10 *
B.1.1.434 1274 6 6.534418 -27.588067 73.176135 1.131378e-11 *
XBB.1.5.92 41 4 6.272764 6.272764 5.454472 5.767535e+03 * *
JE.1.1.1 46 5 5.577102 -11.675249 41.350497 9.234306e-05 * *
LE.1.2 19 5 5.362692 -12.680191 43.360383 3.380168e-05 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 272.723168 NaN NaN NaN * * *
LF.7 58 8 262.666982 267.385801 -184.771602 4.361977e-05 * *
XFG.2 500 8 245.322126 250.010745 -150.021491 1.241129e-12 *
XFG.3.1 87 8 228.559265 233.278084 -116.556168 6.730853e-20 *
XFG.1 14 8 212.633263 217.352082 -84.704165 8.123796e-27 *
LF.7.1.8 44 16 184.917733 182.978160 -15.956320 9.617399e-42
LF.7.1 165 16 165.740514 163.861961 22.276079 4.779111e-50
LF.7.7.1 188 34 163.425568 156.919941 36.160117 4.627468e-53
LF.7.1.2 26 16 161.575508 159.673523 30.652954 7.274862e-52
LF.7.1.5 40 16 151.940084 150.116541 49.766919 5.128254e-56



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29734_29759

Case 58 (XFG): USA/NY-PRL-250708_81F10/2025


Target: 530 samples Number of changes: 151
BC: LD.1 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-151Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.19e-197Rec. model vs L2: 1.33e-07
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LD.1 70 4 9.085704 NaN NaN NaN * * *
XEC.29 135 4 8.457912 8.457912 -8.915824 0.535261 * *
BA.5.1.17 357 3 8.456578 -1.543422 11.086845 0.000024 * *
JN.1.29 69 4 7.971640 7.971640 -7.943281 0.327915 * *
KP.2 1589 5 7.815486 6.243829 -4.487657 0.058426 * *
MC.8 93 4 7.731975 7.731975 -7.463950 0.257947 * *
XEC.39 155 4 7.208205 7.208205 -6.416409 0.153355 * *
MC.9 298 4 6.547233 6.547233 -5.094467 0.078866 * *
MC.2 396 4 6.252566 6.252566 -4.505133 0.059013 * *
MC.1 932 4 6.073660 6.073660 -4.147321 0.049292 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 292.228759 NaN NaN NaN * * *
LF.7 58 6 288.888377 278.888377 -215.776754 3.543696e-02 * *
XFG.2 500 6 277.620087 269.918994 -197.837988 4.506454e-06 *
XFG.3.1 87 6 269.640359 259.640359 -177.280718 1.546278e-10 *
XFG.1 14 6 253.714357 243.714357 -145.428715 1.875634e-17 *
LF.7.7.1 188 14 211.719025 183.341668 -24.683335 1.128804e-43
LF.7.1 165 14 209.808982 201.200980 -60.401960 6.443445e-36
LF.7.1.8 44 14 201.708175 182.172322 -22.344644 3.503436e-44
LF.7.6 15 14 198.460035 178.924182 -15.848364 1.365239e-45
LF.7.3 54 14 195.118331 175.506628 -9.013256 4.466028e-47



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26749_T|C, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28010_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250708_81F10/2025


Target: 530 samples Number of changes: 151
BC: LD.1 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-151Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.19e-197Rec. model vs L2: 1.33e-07
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LD.1 70 4 9.085704 NaN NaN NaN * * *
XEC.29 135 4 8.457912 8.457912 -8.915824 0.535261 * *
BA.5.1.17 357 3 8.456578 -1.543422 11.086845 0.000024 * *
JN.1.29 69 4 7.971640 7.971640 -7.943281 0.327915 * *
KP.2 1589 5 7.815486 6.243829 -4.487657 0.058426 * *
MC.8 93 4 7.731975 7.731975 -7.463950 0.257947 * *
XEC.39 155 4 7.208205 7.208205 -6.416409 0.153355 * *
MC.9 298 4 6.547233 6.547233 -5.094467 0.078866 * *
MC.2 396 4 6.252566 6.252566 -4.505133 0.059013 * *
MC.1 932 4 6.073660 6.073660 -4.147321 0.049292 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 292.228759 NaN NaN NaN * * *
LF.7 58 6 288.888377 278.888377 -215.776754 3.543696e-02 * *
XFG.2 500 6 277.620087 269.918994 -197.837988 4.506454e-06 *
XFG.3.1 87 6 269.640359 259.640359 -177.280718 1.546278e-10 *
XFG.1 14 6 253.714357 243.714357 -145.428715 1.875634e-17 *
LF.7.7.1 188 14 211.719025 183.341668 -24.683335 1.128804e-43
LF.7.1 165 14 209.808982 201.200980 -60.401960 6.443445e-36
LF.7.1.8 44 14 201.708175 182.172322 -22.344644 3.503436e-44
LF.7.6 15 14 198.460035 178.924182 -15.848364 1.365239e-45
LF.7.3 54 14 195.118331 175.506628 -9.013256 4.466028e-47



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22567_G|T,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26749_T|C, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28010_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250715_81G02/2025


Target: 530 samples Number of changes: 153
BC: LF.7 + KP.3.1.5 + LF.7BC BR: 4-5, 7-8 BC BR coord: 2487 - 2488, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-153Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02
Rec. model vs L1: 5.52e-09Rec. model vs L2: 2.84e-220
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 3 4.718819 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 7.613984 -7.227967 1.000000 * *
NL.11 57 5 7.208518 7.208518 -6.417037 0.666977 * *
XBB.4 49 4 6.609415 3.722163 0.555673 0.020343 * *
B.1.1.304 143 6 6.536776 -3.463224 14.926449 0.000015 * *
AZ.5 21 6 6.536776 -3.463224 14.926449 0.000015 * *
B.1.1.434 1274 6 6.534418 -3.465582 14.931164 0.000015 * *
XBB.1.5.92 41 4 6.272764 3.900411 0.199177 0.024355 * *
JE.1.1.1 46 5 5.577102 5.577102 -3.154203 0.130029 * *
LE.1.2 19 5 5.362692 -2.680191 13.360383 0.000034 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 8 282.666982 NaN NaN NaN * * *
XFG.3 480 8 281.735746 276.439919 -204.879838 3.886796e-01 * *
XFG.2 500 8 265.322126 260.010745 -172.021491 2.845335e-08 *
XFG.3.1 87 8 248.559265 243.278084 -138.556168 1.543074e-15 *
XFG.1 14 8 232.633263 227.352082 -106.704165 1.862411e-22 *
LF.7.1.8 44 16 204.917733 192.978160 -37.956320 2.204826e-37
LF.7.1 165 16 185.740514 173.861961 0.276079 1.095630e-45
LF.7.7.1 188 12 182.783973 166.919941 14.160117 1.060865e-48
LF.7.1.2 26 16 181.575508 169.673523 8.652954 1.667790e-47
LF.7.1.5 40 16 171.940084 160.116541 27.766919 1.175672e-51



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250715_81G02/2025


Target: 530 samples Number of changes: 153
BC: LF.7 + KP.3.1.5 + LF.7BC BR: 4-5, 7-8 BC BR coord: 2487 - 2488, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-153Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02
Rec. model vs L1: 5.52e-09Rec. model vs L2: 2.84e-220
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 3 4.718819 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 7.613984 -7.227967 1.000000 * *
NL.11 57 5 7.208518 7.208518 -6.417037 0.666977 * *
XBB.4 49 4 6.609415 3.722163 0.555673 0.020343 * *
B.1.1.304 143 6 6.536776 -3.463224 14.926449 0.000015 * *
AZ.5 21 6 6.536776 -3.463224 14.926449 0.000015 * *
B.1.1.434 1274 6 6.534418 -3.465582 14.931164 0.000015 * *
XBB.1.5.92 41 4 6.272764 3.900411 0.199177 0.024355 * *
JE.1.1.1 46 5 5.577102 5.577102 -3.154203 0.130029 * *
LE.1.2 19 5 5.362692 -2.680191 13.360383 0.000034 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 8 282.666982 NaN NaN NaN * * *
XFG.3 480 8 281.735746 276.439919 -204.879838 3.886796e-01 * *
XFG.2 500 8 265.322126 260.010745 -172.021491 2.845335e-08 *
XFG.3.1 87 8 248.559265 243.278084 -138.556168 1.543074e-15 *
XFG.1 14 8 232.633263 227.352082 -106.704165 1.862411e-22 *
LF.7.1.8 44 16 204.917733 192.978160 -37.956320 2.204826e-37
LF.7.1 165 16 185.740514 173.861961 0.276079 1.095630e-45
LF.7.7.1 188 12 182.783973 166.919941 14.160117 1.060865e-48
LF.7.1.2 26 16 181.575508 169.673523 8.652954 1.667790e-47
LF.7.1.5 40 16 171.940084 160.116541 27.766919 1.175672e-51



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250722_81C08/2025


Target: 530 samples Number of changes: 157
BC: KS.1.3 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,9-157Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.02e-222Rec. model vs L2: 1.13e-08
Flags: Model_2BP_Bad_L1_opp

KS.1.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1.3 45 4 10.286720 NaN NaN NaN * * *
KP.3.1 1957 8 8.879327 4.771811 -1.543623 0.004026 *
KP.3.2.9 28 4 8.768748 8.768748 -9.537496 0.219808 * *
LK.2.1 10 4 8.699755 8.699755 -9.399510 0.204948 * *
PR.2 20 4 8.648462 8.648462 -9.296923 0.194952 * *
KR.1.1 33 4 8.541924 8.541924 -9.083849 0.174645 * *
JN.2.5 25 4 8.435789 8.435789 -8.871579 0.157237 * *
KP.2.15 253 4 8.319432 8.319432 -8.638864 0.140156 * *
JN.1.16.5 24 4 7.781727 7.781727 -7.563453 0.081676 * *
LF.7.3.1 26 4 7.705023 7.705023 -7.410046 0.075774 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 9 279.302040 NaN NaN NaN * * *
XFG.2 500 9 247.105743 230.750611 -107.501222 5.320311e-18 *
LF.7 58 9 237.824674 218.888377 -83.776754 3.760144e-23 *
XFG.3.1 87 18 218.660957 199.640359 -45.280718 1.640724e-31
XFG.1 14 18 203.954846 183.714357 -13.428715 1.990197e-38
LF.7.1.8 44 18 198.438621 162.930832 28.138336 1.871049e-47
LF.7.7.1 188 18 197.651096 159.029161 35.941678 3.787361e-49
LF.7.1 165 18 180.136870 144.651137 64.697727 2.153685e-55
LF.7.6 15 18 162.806258 133.025828 87.948344 1.925346e-60
LF.7.1.2 26 18 162.320821 126.781111 100.437778 3.735422e-63



Target sequence

, 241_C|T, 313_C|T, 670_T|G, 897_C|A, 934_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4584_A|G, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T,
8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 16376_C|T, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20825_C|T, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22001_A|G, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23601_C|T,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250722_81F09/2025


Target: 530 samples Number of changes: 152
BC: LD.1 + XFG.3 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-152Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.19e-197Rec. model vs L2: 1.33e-07
Flags: Model_2BP_Bad_L1_opp

LD.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LD.1 70 4 9.085704 NaN NaN NaN * * *
XEC.29 135 4 8.457912 8.457912 -8.915824 0.535261 * *
BA.5.1.17 357 3 8.456578 -1.543422 11.086845 0.000024 * *
JN.1.29 69 4 7.971640 7.971640 -7.943281 0.327915 * *
KP.2 1589 5 7.815486 6.243829 -4.487657 0.058426 * *
MC.8 93 4 7.731975 7.731975 -7.463950 0.257947 * *
XEC.39 155 4 7.208205 7.208205 -6.416409 0.153355 * *
MC.9 298 4 6.547233 6.547233 -5.094467 0.078866 * *
MC.2 396 4 6.252566 6.252566 -4.505133 0.059013 * *
MC.1 932 4 6.073660 6.073660 -4.147321 0.049292 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 282.228759 NaN NaN NaN * * *
LF.7 58 6 278.888377 268.888377 -193.776754 3.543696e-02 * *
XFG.2 500 6 267.620087 259.918994 -175.837988 4.506454e-06 *
XFG.3.1 87 6 259.640359 249.640359 -155.280718 1.546278e-10 *
XFG.1 14 6 243.714357 233.714357 -123.428715 1.875634e-17 *
LF.7.7.1 188 14 201.719025 173.341668 -2.683335 1.128804e-43
LF.7.1 165 14 199.808982 191.200980 -38.401960 6.443445e-36
LF.7.1.8 44 14 191.708175 172.172322 -0.344644 3.503436e-44
LF.7.6 15 14 188.460035 168.924182 6.151636 1.365239e-45
LF.7.3 54 14 185.118331 165.506628 12.986744 4.466028e-47



Target sequence

, 241_C|T, 606_T|C, 670_T|G, 897_C|A, 1288_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4901_C|A, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15327_G|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22567_G|T, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26749_T|C, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28010_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29137_C|T, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250728_81D05/2025


Target: 530 samples Number of changes: 154
BC: XFG.3 + KP.3.1.5 + XFG.3BC BR: 3-4, 7-8 BC BR coord: 896 - 897, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-154Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.82e-02
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 3.30e-201
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 -2.386016 22.772033 1.000000e+00 * *
NL.11 57 5 7.208518 -2.791482 23.582963 6.669768e-01 * *
XBB.4 49 4 6.609415 6.609415 4.781171 8.062670e+03 * *
B.1.1.304 143 6 6.536776 -19.539319 57.078638 3.545505e-08 *
AZ.5 21 6 6.536776 -23.368480 64.736960 7.697156e-10 *
B.1.1.434 1274 6 6.534418 -27.588067 73.176135 1.131378e-11 *
XBB.1.5.92 41 4 6.272764 6.272764 5.454472 5.767535e+03 * *
JE.1.1.1 46 5 5.577102 -11.675249 41.350497 9.234306e-05 * *
LE.1.2 19 5 5.362692 -12.680191 43.360383 3.380168e-05 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 232.800723 NaN NaN NaN * * *
LF.7 58 8 219.299864 224.018683 -86.037366 1.391678e-06 *
XFG.2 500 8 206.201918 210.890537 -59.781074 2.762182e-12 *
XFG.3.1 87 8 204.183727 208.902547 -55.805093 3.794703e-13 *
XFG.1 14 8 142.417961 147.136780 67.726439 5.659886e-40 *
LF.7.1.8 44 16 140.641999 138.702426 84.595149 1.228949e-43
LF.7.1 165 16 123.055570 121.177017 119.645967 3.009698e-51
LF.7.7.1 188 34 121.195120 114.689494 132.621012 4.593283e-54
LF.7.3.1 26 16 113.050269 115.717675 130.564651 1.286609e-53
LF.7.1.5 40 54 111.611145 79.901239 202.197523 3.572878e-69



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16064_A|G, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24769_T|C, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250728_81H09/2025


Target: 530 samples Number of changes: 148
BC: XFG.3 + XBB.1.42.1 + XFG.3BC BR: 135-136, 140-141 BC BR coord: 27808 - 27809, 28361 - 28362
Direction L1: >> Initial region span: 1-135,137-140,141-148Gap history (edge excluded): 135-141 -> 135-137
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.00e-06
Rec. model vs L1: 1.26e-07 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 135 265.894236 NaN NaN NaN * * *
LF.7 58 135 252.901546 264.770108 -189.540216 2.155657e-07 *
XFG.3.1 87 135 251.650859 265.211030 -190.422060 3.347105e-07 *
XFG.2 500 135 249.547299 263.886110 -187.772220 8.896703e-08 *
LF.7.1.8 44 135 194.127090 192.391476 -44.782951 7.931313e-39 *
XFG.1 14 135 174.651239 189.115097 -38.230193 2.999374e-40 *
LF.7.1 165 135 163.846563 173.779337 -7.558674 6.563338e-47 *
LF.7.7.1 188 147 161.559857 164.299140 11.401720 5.012024e-51
LF.7.3.1 26 135 159.503538 157.695991 24.608018 6.784191e-54 *
LF.7.3 54 135 149.789073 148.170299 43.659403 4.952712e-58 *
|||||

XBB.1.42.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.1.42.1 91 137 10.168975 NaN NaN NaN * * *
LF.7.6.1 26 137 10.035444 -13.338585 42.677171 0.000035 * *
FL.1.3 49 137 9.401720 -3.850097 23.700193 0.458406 * *
LF.7.7.1 188 137 8.057099 -5.557252 27.114504 0.083326 * *
FL.15.1.1 198 137 8.005274 -5.246543 26.493087 0.113608 * *
HF.1.1 292 137 7.616787 -5.635030 27.270060 0.076919 * *
EG.5.2 295 137 7.606565 -5.645252 27.290503 0.076154 * *
NB.1.8.1 357 137 7.415805 -6.198546 28.397091 0.043718 * *
EG.6.1 838 137 7.255670 -5.993758 27.987515 0.053665 * *
XBB.1.9.1 1695 137 7.235525 -6.012746 28.025492 0.052602 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 141 14.226904 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2698_T|C, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10744_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12459_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23487_T|G, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|A, 28271_A|T, 28297_T|C,
28311_C|T, 28340_T|C, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250728_82B06/2025


Target: 530 samples Number of changes: 153
BC: XFG.3 + KP.3.1.5 + XFG.3BC BR: 3-4, 7-8 BC BR coord: 896 - 897, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-153Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.82e-02
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 3.30e-201
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 -2.386016 22.772033 1.000000e+00 * *
NL.11 57 5 7.208518 -2.791482 23.582963 6.669768e-01 * *
XBB.4 49 4 6.609415 6.609415 4.781171 8.062670e+03 * *
B.1.1.304 143 6 6.536776 -19.539319 57.078638 3.545505e-08 *
AZ.5 21 6 6.536776 -23.368480 64.736960 7.697156e-10 *
B.1.1.434 1274 6 6.534418 -27.588067 73.176135 1.131378e-11 *
XBB.1.5.92 41 4 6.272764 6.272764 5.454472 5.767535e+03 * *
JE.1.1.1 46 5 5.577102 -11.675249 41.350497 9.234306e-05 * *
LE.1.2 19 5 5.362692 -12.680191 43.360383 3.380168e-05 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 242.800723 NaN NaN NaN * * *
LF.7 58 8 229.299864 234.018683 -106.037366 1.391678e-06 *
XFG.2 500 8 216.201918 220.890537 -79.781074 2.762182e-12 *
XFG.3.1 87 8 214.183727 218.902547 -75.805093 3.794703e-13 *
XFG.1 14 8 152.417961 157.136780 47.726439 5.659886e-40 *
LF.7.1.8 44 16 150.641999 148.702426 64.595149 1.228949e-43
LF.7.1 165 16 133.055570 131.177017 99.645967 3.009698e-51
LF.7.7.1 188 34 131.195120 124.689494 112.621012 4.593283e-54
LF.7.3.1 26 16 123.050269 125.717675 110.564651 1.286609e-53
LF.7.7.2 239 12 114.883598 109.063369 143.873263 7.520937e-61



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9598_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12754_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28857_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250728_82C09/2025


Target: 530 samples Number of changes: 150
BC: XFG.3 + KP.3.1.5 + XFG.3BC BR: 3-4, 7-8 BC BR coord: 896 - 897, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-150Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.82e-02
Rec. model vs L1: 5.55e-09 Rec. model vs L2: 3.33e-195
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 -2.386016 22.772033 1.000000e+00 * *
NL.11 57 5 7.208518 -2.791482 23.582963 6.669768e-01 * *
XBB.4 49 4 6.609415 6.609415 4.781171 8.062670e+03 * *
B.1.1.304 143 6 6.536776 -19.539319 57.078638 3.545505e-08 *
AZ.5 21 6 6.536776 -23.368480 64.736960 7.697156e-10 *
B.1.1.434 1274 6 6.534418 -27.588067 73.176135 1.131378e-11 *
XBB.1.5.92 41 4 6.272764 6.272764 5.454472 5.767535e+03 * *
JE.1.1.1 46 5 5.577102 -11.675249 41.350497 9.234306e-05 * *
LE.1.2 19 5 5.362692 -12.680191 43.360383 3.380168e-05 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 261.813302 NaN NaN NaN * * *
LF.7 58 8 259.299864 264.018683 -172.037366 8.249645e-02 * *
XFG.2 500 8 246.201918 250.890537 -145.781074 1.637377e-07 *
XFG.3.1 87 8 244.183727 248.902547 -141.805093 2.249439e-08 *
XFG.1 14 8 182.417961 187.136780 -18.273561 3.355089e-35 *
LF.7.1.8 44 16 180.641999 178.702426 -1.404851 7.285009e-39
LF.7.1 165 16 163.055570 161.177017 33.645967 1.784100e-46
LF.7.7.1 188 12 160.553525 154.689494 46.621012 2.722824e-49
LF.7.3.1 26 16 153.050269 155.717675 44.564651 7.626809e-49
LF.7.7.2 239 12 144.883598 139.063369 77.873263 4.458290e-56



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C,
23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T,
27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/NY-PRL-250728_82D06/2025


Target: 530 samples Number of changes: 149
BC: XFG.3 + XDD.1.1 + XFG.3BC BR: 136-137, 142-143 BC BR coord: 27915 - 27916, 28880 - 28881
Direction L1: >> Initial region span: 1-136,138-142,143-149Gap history (edge excluded): 136-143 -> 136-138
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.15e-07
Rec. model vs L1: 1.58e-07 Rec. model vs L2: 5.93e-323
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 136 258.237613 NaN NaN NaN * * *
LF.7 58 136 256.515897 267.640847 -195.281693 1.592285e-02 * *
XFG.2 500 136 253.161649 266.725765 -193.451530 6.377367e-03 * *
XFG.3.1 87 136 240.935043 253.891959 -167.783917 1.700089e-08 *
XFG.1 14 136 178.265589 191.950744 -43.901488 2.139299e-35 *
LF.7.1.8 44 136 170.738844 168.224526 3.550948 1.063249e-45 *
LF.7.1 165 136 167.460914 176.639525 -13.279050 4.799798e-42 *
LF.7.3.1 26 136 163.117889 160.654240 18.691519 5.483094e-49 *
LF.7.7.1 188 136 162.823905 167.134787 5.730425 3.574818e-46 *
LF.7.3 54 136 153.403424 151.024638 37.950724 3.603876e-53 *
|||||

XDD.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XDD.1.1 29 138 13.385163 NaN NaN NaN * * *
JG.3 1482 138 10.138247 0.138247 17.723506 3.896856e-02 * *
HK.3 1830 138 9.256169 -0.743831 19.487662 1.608288e-02 * *
JN.1.3 111 140 8.464940 -16.336019 50.672039 2.727174e-09
XBB.1.5.43 48 140 8.201786 -11.033084 40.066167 5.463533e-07
GK.2.1 255 138 7.855661 -8.235089 34.470179 8.984587e-06 *
BW.1 131 140 7.218843 -12.016026 42.032053 2.050525e-07
XBB.1.16.6 4784 137 6.553074 6.553074 4.893853 2.380748e+01 * *
BA.2.76 427 140 6.030217 -13.204653 44.409305 6.238132e-08
BA.2.36 3016 140 5.869129 -13.366736 44.733472 5.315785e-08
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 143 13.542054 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 4822_A|G, 5239_C|T, 6183_A|G, 6351_A|G, 6777_A|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9989_A|G, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 16986_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21610_T|C, 21641_G|T, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28268_A|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/OSPHL10334/2025


Target: 530 samples Number of changes: 148
BC: EG.5.1.16 + XFG.3 BC BR: 5-6 BC BR coord: 2512 - 2513
Direction L1: << Initial region span: 1-5,6-148Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 9.53e-23
Flags: Model_2BP_Bad_L1_opp

EG.5.1.16 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
EG.5.1.16 519 5 6.229741 NaN NaN NaN * * *
EG.5.2 295 5 6.214795 6.214795 5.570409 9.851119e-01 * *
HK.27.1 107 4 5.873577 -4.126423 26.252847 3.183323e-05 * *
JN.11 67 3 5.085550 -18.541804 55.083609 1.747937e-11
KP.2.3.10 10 3 4.790433 -18.836921 55.673843 1.301394e-11
HK.29 238 4 4.691106 -5.308894 28.617788 9.732887e-06 *
DN.3 10 3 4.685073 -18.767248 55.534496 1.395756e-11
BF.5.5 91 3 4.661600 -18.338270 54.676541 2.134935e-11
PL.1.1 12 3 4.608112 -19.019243 56.038486 1.081594e-11
BN.1.1.1 41 3 4.453366 -15.546634 49.093268 3.493314e-10
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 6 333.613273 NaN NaN NaN * * *
LF.7 58 6 333.571870 333.571870 -335.143740 9.559975e-01 * *
XFG.2 500 5 329.187907 328.801106 -325.602212 8.107222e-03 * *
XFG.3.1 87 6 301.566276 301.566276 -271.132551 1.204653e-14 *
XFG.1 14 6 284.571728 284.571728 -237.143455 5.012185e-22 *
LF.7.1 165 12 242.566038 241.941555 -151.883111 1.534806e-40
LF.7.7.1 188 12 238.986556 229.544250 -127.088501 6.352918e-46
LF.7.1.8 44 12 235.721266 235.115133 -138.230265 1.667222e-43
LF.7.6 15 12 220.487112 219.880978 -107.761956 4.031968e-50
LF.7.3 54 12 217.040048 216.358064 -100.716127 1.193440e-51



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 2334_C|T, 2509_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C

Case 58 (XFG): USA/NY-PRL-250715_81G02/2025


Target: 530 samples Number of changes: 153
BC: LF.7 + KP.3.1.5 + LF.7BC BR: 4-5, 7-8 BC BR coord: 2487 - 2488, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-153Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.72e-02
Rec. model vs L1: 5.52e-09Rec. model vs L2: 2.84e-220
Flags: Model_2BP_Best

LF.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 3 4.718819 None None None * * *
|||||

KP.3.1.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.5 45 5 7.613984 NaN NaN NaN * * *
XBB.2.3.14 18 5 7.613984 7.613984 -7.227967 1.000000 * *
NL.11 57 5 7.208518 7.208518 -6.417037 0.666977 * *
XBB.4 49 4 6.609415 3.722163 0.555673 0.020343 * *
B.1.1.304 143 6 6.536776 -3.463224 14.926449 0.000015 * *
AZ.5 21 6 6.536776 -3.463224 14.926449 0.000015 * *
B.1.1.434 1274 6 6.534418 -3.465582 14.931164 0.000015 * *
XBB.1.5.92 41 4 6.272764 3.900411 0.199177 0.024355 * *
JE.1.1.1 46 5 5.577102 5.577102 -3.154203 0.130029 * *
LE.1.2 19 5 5.362692 -2.680191 13.360383 0.000034 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 8 282.666982 NaN NaN NaN * * *
XFG.3 480 8 281.735746 276.439919 -204.879838 3.886796e-01 * *
XFG.2 500 8 265.322126 260.010745 -172.021491 2.845335e-08 *
XFG.3.1 87 8 248.559265 243.278084 -138.556168 1.543074e-15 *
XFG.1 14 8 232.633263 227.352082 -106.704165 1.862411e-22 *
LF.7.1.8 44 16 204.917733 192.978160 -37.956320 2.204826e-37
LF.7.1 165 16 185.740514 173.861961 0.276079 1.095630e-45
LF.7.7.1 188 12 182.783973 166.919941 14.160117 1.060865e-48
LF.7.1.2 26 16 181.575508 169.673523 8.652954 1.667790e-47
LF.7.1.5 40 16 171.940084 160.116541 27.766919 1.175672e-51



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6539_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17007_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19593_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23148_A|C, 23222_G|A, 23271_C|T, 23277_C|T, 23373_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25352_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27754_G|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): USA/VT-25-006305-WGS-01/2025


Target: 530 samples Number of changes: 148
BC: MC.20 + XFG.3 BC BR: 3-4 BC BR coord: 865 - 866
Direction L1: << Initial region span: 1-3,4-148Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.28e-230Rec. model vs L2: 5.60e-09
Flags: Model_2BP_Bad_L1_opp

MC.20 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.20 14 3 8.387412 NaN NaN NaN * * *
BA.5.2.28 894 3 6.014678 6.014678 -4.029355 0.093481 * *
CQ.2 434 3 5.942716 5.942716 -3.885432 0.087161 * *
BA.5.2.12 97 3 5.758611 5.758611 -3.517223 0.072440 * *
XEC.2.1 265 3 5.572695 5.572695 -3.145391 0.060205 * *
PA.1.3 18 3 5.497040 5.497040 -2.994081 0.055576 * *
GK.1.6 51 3 5.192024 5.192024 -2.384049 0.040967 * *
JN.1.37 26 3 5.129316 5.129316 -2.258631 0.038581 * *
HK.3.2 356 3 5.118018 5.118018 -2.236036 0.038197 * *
MS.1 34 3 4.861052 4.861052 -1.722103 0.029452 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 4 280.901341 NaN NaN NaN * * *
LF.7 58 4 280.213079 280.213079 -218.426158 5.040902e-01 * *
XFG.2 500 16 275.212650 269.131672 -196.263343 7.733106e-06
XFG.3.1 87 4 247.532327 247.532327 -153.064655 3.218053e-15 *
XFG.1 14 16 232.793190 231.282640 -120.565280 2.834518e-22
LF.7.1.8 44 18 218.942307 195.673532 -49.347064 9.710750e-38
LF.7.1 165 18 211.647267 188.471569 -34.943139 7.213749e-41
LF.7.7.1 188 28 199.925659 170.882672 0.234656 1.663767e-48
LF.7.6 15 10 184.993709 180.691948 -19.383895 3.015435e-44
LF.7.1.2 26 18 182.863442 159.648486 22.703028 2.196818e-53



Target sequence

, 241_C|T, 670_T|G, 853_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6543_C|T, 7869_C|T, 8152_C|T, 8293_C|T, 8350_T|C, 8393_G|A, 8818_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10039_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15381_C|A, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25244_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): IGS-10285-CVDP-0E8038B3-F107-4098-A428-711708784AC4


Target: 530 samples Number of changes: 151
BC: XFG.2 + KP.3.1.1 BC BR: 142-143 BC BR coord: 28361 - 28362
Direction L1: >> Initial region span: 1-142,144-151Gap history (edge excluded): 142-144
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.73e-06 Rec. model vs L2: 1.30e-141
Flags: Model_2BP_Bad_L1_opp

XFG.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.2 500 142 311.047405 NaN NaN NaN * * *
LF.7 58 142 309.587062 309.587062 -295.174125 2.322363e-01 * *
XFG.3 480 148 308.417909 307.128912 -290.257824 1.994055e-02 *
XFG.3.1 87 148 275.208799 273.919801 -223.839603 7.530388e-17
XFG.1 14 148 259.534111 258.245114 -192.490229 1.172874e-23
LF.7.1.8 44 142 224.571938 224.571938 -125.143877 2.782176e-38 *
LF.7.1 165 142 219.939926 219.939926 -115.879851 2.713946e-40 *
LF.7.6 15 142 216.244100 216.244100 -108.488200 6.743465e-42 *
LF.7.7.1 188 142 214.706097 214.706097 -105.412194 1.445671e-42 *
LF.7.3 54 142 206.001218 206.001218 -88.002436 2.396272e-46 *
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 144 9.673219 NaN NaN NaN * * *
XBB.1.18.1 84 149 9.477560 -18.867943 65.735886 8.830979e-09
JN.1.46 308 149 7.040837 -7.696366 43.392731 6.298682e-04 *
BQ.1.1.13 384 149 6.727103 -25.186222 78.372445 1.597494e-11
DV.6 1051 149 5.873972 -22.486817 72.973635 2.377028e-10
JF.1.1 935 149 5.815039 -23.857788 75.715577 6.010068e-11
BF.5 7920 149 4.715060 -22.241819 72.483639 3.036942e-10
BF.7 11554 149 4.391464 -18.808267 65.616534 9.377056e-09
BA.2.9 75328 149 4.282623 -5.604268 39.208536 5.092431e-03 *
NL.14 12 144 3.685154 -6.314846 40.629691 2.503664e-03 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3912_C|A, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 5907_C|T, 6183_A|G, 7279_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28467_A|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29436_A|G, 29510_A|C, 29734_29759

Case 58 (XFG): IGS-10285-CVDP-34E9F1FA-26B3-4AD3-BB29-6A6F16FA356F


Target: 530 samples Number of changes: 153
BC: XFG.3 + BY.1 + XFG.3 BC BR: 3-4, 6-7 BC BR coord: 896 - 897, 2909 - 2910
Direction L1: << Initial region span: 1-3,4-6,7-153Gap history (edge excluded): 3-7 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.57e-07
Rec. model vs L1: 5.75e-15Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

BY.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BY.1 185 6 9.220286 NaN NaN NaN * * *
EG.6.1.1 59 5 6.002246 -3.997754 17.995507 1.813957e-06 *
EG.6.1 838 5 5.981751 -4.018249 18.036497 1.778038e-06 *
BA.4.5 49 5 5.981627 -4.018373 18.036746 1.778038e-06 *
XFG.1 14 5 4.972627 -5.027373 20.054746 6.508413e-07 *
XCT.1 42 4 4.925038 -15.259019 40.518038 2.335991e-11
JG.4 61 4 4.925038 -15.225683 40.451365 2.419198e-11
B.1.258.16 10 4 4.925038 -15.074962 40.149923 2.810707e-11
AY.47 22935 4 4.917818 -15.082182 40.164364 2.796688e-11
XDK.1 127 5 4.745072 -5.254928 20.509857 5.171153e-07 *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 283.957599 NaN NaN NaN * * *
LF.7 58 7 281.317960 286.036780 -224.073559 7.243976e-02 * *
XFG.2 500 7 280.041205 284.729825 -221.459650 1.964367e-02 * *
XFG.1 14 7 272.328306 277.047125 -206.094250 9.029622e-06 *
XFG.3.1 87 7 261.080690 265.799509 -183.599019 1.180397e-10 *
LF.7.7.1 188 12 196.168587 190.308442 -32.616884 1.937036e-43
LF.7.1 165 12 194.430741 197.417325 -46.834650 2.359391e-40
LF.7.1.8 44 12 186.068685 189.034653 -30.069306 5.412679e-44
LF.7.6 15 12 182.840632 185.876110 -23.752219 2.296369e-45
LF.7.7.2 239 12 180.400510 174.584167 -1.168335 2.869835e-50



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1684_C|T, 2790_C|T, 2904_T|C, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C, 8393_G|A,
8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10868_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13402_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16224_T|C, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20134_G|T, 20970_C|A, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T,
22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A,
23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26951_G|C,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): IGS-10285-CVDP-6445BD5D-CEF7-4760-9DC3-A57A77560482


Target: 530 samples Number of changes: 155
BC: XFG.3 + CV.1 + XFG.3 BC BR: 3-4, 7-8 BC BR coord: 2474 - 2475, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-7,8-155Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.21e-02
Rec. model vs L1: 5.55e-09Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 3 4.704173 None None None * * *
|||||

CV.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
CV.1 86 5 9.239404 NaN NaN NaN * * *
BM.1.1.3 341 5 9.230568 -0.769432 11.538865 0.990050 * *
BM.1.1.4 18 5 9.182246 -0.817754 11.635508 0.941765 * *
NL.4 115 4 9.133467 9.133467 -8.266935 19830.967301 * *
FL.29 37 5 7.014781 -2.985219 15.970439 0.108067 * *
BA.5.6.1 96 5 6.977641 -3.022359 16.044718 0.104350 * *
FY.5.2 12 5 6.754498 -3.245502 16.491005 0.083326 * *
NA.1 15 5 6.531354 -3.468646 16.937292 0.066537 * *
BQ.1.31 78 6 6.108072 -6.420323 22.840646 0.003483 * *
EG.5.1.6 1581 5 6.047979 -3.952021 17.904043 0.041172 * *
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 281.941538 NaN NaN NaN * * *
XFG.2 500 8 262.481232 267.169851 -186.339703 3.484295e-09 *
LF.7 58 8 261.314074 266.032894 -184.065787 1.119930e-09 *
XFG.3.1 87 17 241.178496 245.795623 -143.591247 1.815810e-18
XFG.1 14 17 227.451939 230.849175 -113.698349 5.868666e-25
LF.7.1 165 17 189.291992 177.413439 -6.826878 3.647655e-48
LF.7.7.1 188 17 185.348216 170.304556 7.390889 2.979751e-51
LF.7.1.8 44 16 182.266109 180.326536 -12.653071 6.695927e-47
LF.7.6 15 17 172.014928 165.872223 16.255553 3.532514e-53
LF.7.1.2 26 17 171.151893 159.249908 29.500184 4.710364e-56



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2675_C|T, 2790_C|T, 3037_C|T, 3130_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 6964_T|C, 7113_C|T, 7842_A|G, 7869_C|T, 8293_C|T,
8350_T|C, 8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14183_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18252_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22419_C|T, 22468_G|T, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22792_C|T, 22813_G|T, 22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28406_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C,
29555_C|T, 29734_29759

Case 58 (XFG): IGS-10285-CVDP-AECC2415-2C37-4298-B483-C570A97B84D9


Target: 530 samples Number of changes: 152
BC: JN.11 + LF.7 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-152Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.94e-228Rec. model vs L2: 4.16e-08
Flags: Model_2BP_Bad_L1_opp

JN.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.11 67 4 8.712905 NaN NaN NaN * * *
KP.2.3.10 10 4 8.417788 8.417788 -8.835576 0.744532 * *
PL.1.1 12 4 8.235466 8.235466 -8.470933 0.618783 * *
PD.2 21 4 7.675851 7.675851 -7.351701 0.353455 * *
KP.4.2.4 22 4 7.629331 7.629331 -7.258661 0.337902 * *
KR.1.4 24 4 7.408788 7.408788 -6.817576 0.271173 * *
KP.3.1.2 28 4 7.277693 7.277693 -6.555386 0.238115 * *
JN.1.69 32 4 7.254637 7.254637 -6.509274 0.232236 * *
JN.1.50.2 33 4 7.162322 7.162322 -6.324644 0.211189 * *
LP.8.1.10 32 4 7.156197 7.156197 -6.312394 0.210136 * *
|||||

LF.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7 58 6 305.993193 NaN NaN NaN * * *
XFG.3 480 6 305.966793 295.966793 -249.933586 9.704455e-01 * *
XFG.2 500 6 301.198751 283.660121 -225.320242 4.395189e-06 *
XFG.3.1 87 6 272.157898 262.157898 -182.315796 2.021372e-15 *
XFG.1 14 6 257.211449 247.211449 -152.422899 6.500454e-22 *
LF.7.1 165 16 219.915996 204.430262 -66.860524 1.713270e-40
LF.7.1.8 44 16 212.916100 197.408311 -52.816622 1.531364e-43
LF.7.7.1 188 12 206.168587 186.726282 -31.452563 3.504628e-48
LF.7.6 15 12 192.840632 182.234498 -22.468997 3.932419e-50
LF.7.1.2 26 16 191.151893 175.612183 -9.224366 5.217456e-53



Target sequence

, 241_C|T, 670_T|G, 683_C|T, 897_C|A, 1349_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7390_C|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16457_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22286_C|A, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T,
22882_T|G, 22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26149_T|C, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 58 (XFG): IGS-10285-CVDP-C599AD85-A1B5-4508-ABD3-28AF4ABD7F3A


Target: 530 samples Number of changes: 150
BC: LB.1.3.5 + XFG.3 BC BR: 5-6 BC BR coord: 2792 - 2793
Direction L1: << Initial region span: 1-5,7-150Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.12e-172Rec. model vs L2: 1.44e-07
Flags: Model_2BP_Bad_L1_opp

LB.1.3.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LB.1.3.5 275 5 12.164161 NaN NaN NaN * * *
MC.19 221 5 9.972804 9.972804 -1.945608 1.119167e-01 * *
LB.1.7 1971 6 8.001031 7.810114 2.379772 1.284244e-02 * *
JN.2 574 4 7.993860 0.921611 16.156779 1.307250e-05 * *
DM.1 33 3 7.229608 -5.145505 28.291011 3.036425e-08
BA.2.38.1 43 3 6.941385 -1.981407 21.962815 7.192909e-07
XBB.1.28 11 3 6.519127 -2.403665 22.807331 4.702506e-07
BQ.1.1.23 644 3 5.352364 -7.019638 32.039276 4.656508e-09
BA.5.1.30 4775 3 4.442524 -4.481106 26.962213 5.904299e-08
BA.4.6.5 1612 3 4.029062 -8.788269 35.576537 7.931569e-10
|||||

XFG.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 7 296.978611 NaN NaN NaN * * *
LF.7 58 7 296.906879 286.906879 -235.813758 9.277435e-01 * *
XFG.2 500 7 291.857845 281.857845 -225.715690 5.976023e-03 * *
XFG.3.1 87 7 266.956245 256.956245 -175.912489 9.126582e-14 *
XFG.1 14 7 247.918714 237.918714 -137.837428 4.937564e-22 *
LF.7.1 165 16 211.677293 195.114352 -52.228703 1.269221e-40
LF.7.1.8 44 16 204.691375 188.106379 -38.212758 1.145864e-43
LF.7.7.1 188 12 197.858755 189.880014 -41.760027 6.760920e-43
LF.7.1.2 26 3 186.521031 180.808011 -23.616022 7.779557e-47
LF.7.6 15 12 184.476889 172.793547 -7.587094 2.570896e-50



Target sequence

, 241_C|T, 514_T|C, 670_T|G, 897_C|A, 2790_C|T, 2857_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4214_T|C, 4321_C|T, 5239_C|T, 6183_A|G, 7760_G|A, 7842_A|G, 7869_C|T, 8293_C|T, 8350_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10369_C|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12865_T|C, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G,
22893_A|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23006_23008, 23012_G|A, 23018_T|C, 23019_T|C,
23021_A|G, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T,
24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29409_C|T, 29510_A|C, 29734_29759

Case 63 (XEK): OZ255297


Target: 289 samples Number of changes: 143
BC: XEK.1 + XEC.2 BC BR: 15-16 BC BR coord: 5705 - 5706
Direction L1: << Initial region span: 1-13,17-143Gap history (edge excluded): 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.83e-01
Rec. model vs L1: 2.00e-15Rec. model vs L2: 2.65e-32
Flags: Model_1BP_Best

XEK.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.1 88 13 27.091884 NaN NaN NaN * * *
XEK.1.2 33 13 27.008002 25.556273 -17.112547 9.277435e-01 * *
XEK.1.1 11 13 18.923304 17.471575 -0.943150 2.858624e-04 * *
XEK.7 12 10 16.741721 7.349839 19.300323 1.151057e-08
XEK.6 23 10 16.697269 7.392398 19.215203 1.198033e-08
XEK.2 67 10 16.597472 7.292601 19.414799 1.089458e-08
JN.1 17255 13 13.628505 -6.371495 46.742989 1.266417e-14 *
XEC.2.1 265 8 13.015012 -29.018407 92.036813 1.844194e-24
KP.3.1.1 12013 14 12.644192 2.644192 28.711616 1.041697e-10 *
KP.2.3 4440 10 12.483385 -15.374951 64.749902 1.555087e-18
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 198.006872 NaN NaN NaN * * *
XEK.1 88 3 196.323932 160.699772 -39.399544 1.385445e-12
KP.3.3 1715 16 191.808188 191.808188 -101.616376 4.492525e+01 * *
XEK.1.2 33 3 188.746271 153.194564 -24.389127 7.624460e-16
XEC.14 193 25 183.025282 156.750509 -31.501018 2.667632e-14
XEK.5 28 3 182.036925 164.678748 -47.357496 7.414489e-11
XEC.31 66 25 180.525047 154.250273 -26.500547 2.189726e-15
XEK.1.1 11 3 179.774906 152.307896 -22.615793 3.146723e-16
XEC.33 169 52 177.108571 145.738331 -9.476661 4.411068e-19
XEC.19 59 25 174.143674 147.868901 -13.737802 3.711855e-18



Target sequence

, 241_C|T, 583_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3774_G|A, 4184_G|A, 4321_C|T, 4921_C|T, 5701_T|C, 5950_G|T, 6183_A|G, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9391_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16575_C|T, 17410_C|T, 18163_A|G, 18354_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19419_G|A, 19716_C|T, 19955_C|T, 20055_A|G, 21641_G|T, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25046_C|T, 25207_C|T, 25584_C|T, 25699_G|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 63 (XEK): USA/2025CV0302/2025


Target: 289 samples Number of changes: 156
BC: XEK.1 + FD.1.1 + XEK.1BC BR: 140-141, 143-144 BC BR coord: 27915 - 27916, 28270 - 28271
Direction L1: >> Initial region span: 1-140,142-143,144-156Gap history (edge excluded): 140-144 -> 140-142
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.14e-03
Rec. model vs L1: 1.08e-15Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEK.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.1 88 140 218.708144 NaN NaN NaN * * *
XEK.5 28 140 197.934589 198.147089 -60.294177 9.077973e-10 *
XEK.6 23 140 185.448321 185.314080 -34.628161 2.432152e-15 *
XEK.1.2 33 140 176.482309 176.653885 -17.307770 4.216970e-19 *
KP.2.3 4440 140 170.440721 172.920295 -9.840590 1.006724e-20 *
KP.3.3 1715 140 170.067375 182.555212 -29.110424 1.539352e-16 *
KP.3.1.1 12013 140 168.159935 175.356906 -14.713813 1.149258e-19 *
XEK.2 67 140 166.916784 167.171613 1.656774 3.204183e-23 *
JN.1 17255 140 157.012071 155.763339 24.473323 3.569347e-28 *
KP.3.1 1957 140 155.848681 160.692312 14.615375 4.914610e-26 *
|||||

FD.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
FD.1.1 218 142 14.812338 NaN NaN NaN * * *
BA.5.1.26 94 142 12.465426 2.465426 1.069148 9.584720e-02 * *
BA.1.9 133 142 9.574093 -0.425907 6.851814 5.326824e-03 * *
JN.1.52 150 142 9.333521 -0.666479 7.332959 4.190229e-03 * *
BA.5.1.9 242 142 8.376916 -1.623084 9.246168 1.604409e-03 * *
CH.1.1.25 271 142 8.150554 -1.849446 9.698893 1.281146e-03 * *
FY.8.1 29 143 7.147088 -12.852912 31.705824 2.129060e-08 *
LP.8.1.1 2345 142 6.607299 -3.392701 12.785403 2.732837e-04 * *
XBB.1.5.72 569 143 6.485511 -13.514489 33.028978 1.100408e-08 *
XBB.1.15.1 11 143 6.037047 -13.962953 33.925906 7.016509e-09 *
|||||

XEK.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.1 88 144 0.25718 None None None * * *



Target sequence

, 241_C|T, 593_C|T, 670_T|G, 829_C|T, 897_C|A, 1905_T|C, 2031_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5392_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10138_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16954_C|T, 17410_C|T, 17550_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21742_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22994_A|G, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23287_T|C, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28039_T|C, 28131_.|T, 28132_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29200_C|T,
29510_A|C, 29734_29759, 29769_C|T

Case 63 (XEK): USA/CA-CDPH-500147163/2025


Target: 289 samples Number of changes: 155
BC: XEC.18 + KP.2.3 + XEC.18BC BR: 4-5, 38-39 BC BR coord: 896 - 897, 12788 - 12789
Direction L1: << Initial region span: 1-4,21-38,39-155Gap history (edge excluded): 4-39 -> 4-21
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.76e-04
Rec. model vs L1: 3.07e-45 Rec. model vs L2: 2.01e-60
Flags: Model_2BP_Best

XEC.18 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 4 5.612364 None None None * * *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 21 22.489705 NaN NaN NaN * * *
KP.2.3.9 23 21 17.600501 -58.325561 192.651121 4.398931e-16 *
LF.1.1 15 35 14.962994 -100.362404 276.724808 2.442185e-34
KP.2.5 66 35 14.159269 -83.013448 242.026896 8.329451e-27
JN.1 17255 22 13.638522 -1.820132 79.640265 1.524603e+09 * *
JN.1.4 8971 22 12.484046 -2.778694 81.557388 5.837597e+08 * *
KP.2.3.3 149 21 12.363388 -63.576142 203.152283 2.308347e-18 *
KP.3.1.1 12013 21 12.232672 -2.561748 81.123495 7.274094e+08 * *
JN.1.38 247 35 12.157599 -76.653630 229.307260 4.816475e-24
JN.1.18.3 97 26 9.481472 -64.858185 205.716370 6.386055e-19
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 39 218.477804 NaN NaN NaN * * *
XEC.2 921 21 215.781251 213.040631 -168.081261 1.588715e-05 *
XEC.2.3 28 39 213.459445 208.178265 -158.356529 1.231331e-07 *
XEC.8 592 39 213.200473 217.478622 -176.957244 1.346832e-03 * *
XEC.2.1 265 58 206.298206 210.450130 -162.900260 1.191855e-06
XEC.33 169 39 202.522247 197.211178 -136.422356 2.119163e-12 *
KP.3.3 1715 21 200.745506 194.730451 -131.460901 1.774655e-13
XEC.40 52 39 197.970137 192.650121 -127.300241 2.217081e-14 *
XEC.36 30 39 197.663987 192.382806 -126.765612 1.700957e-14 *
XEK.1 88 21 196.758634 203.292911 -148.585821 9.307783e-10



Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3736_C|T, 3909_T|C, 4184_G|A, 4321_C|T, 4825_T|C, 5622_C|T, 5701_T|C, 5761_G|A, 6183_A|G, 6601_A|G,
7105_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 9808_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10969_C|T, 11042_G|T, 11288_11296, 11727_G|A,
12544_A|G, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19287_T|A, 19716_C|T, 19955_C|T, 20055_A|G,
21302_C|T, 21304_C|A, 21305_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28057_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29380_A|G,
29510_A|C

Case 63 (XEK): USA/CA-LACPHL-AY11146/2025


Target: 289 samples Number of changes: 148
BC: XEK.1 + KP.2.6.2 BC BR: 145-146 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-145,146-148Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.28e-09 Rec. model vs L2: 4.25e-183
Flags: Model_2BP_Bad_L1_opp

XEK.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.1 88 145 262.588514 NaN NaN NaN * * *
XEK.5 28 145 249.494215 249.494215 -172.988430 2.055482e-06 *
XEK.6 23 145 247.789937 247.789937 -169.579875 3.736299e-07 *
XEK.2 67 145 242.190232 242.190232 -158.380463 1.381633e-09 *
XEK.1.2 33 145 239.778065 239.778065 -153.556130 1.240917e-10 *
XEK.1.1 11 145 230.983464 230.983464 -135.966929 1.879849e-14 *
KP.3.3 1715 148 223.631688 221.329767 -116.659534 1.205063e-18
XEC.2 921 148 210.420146 207.851622 -89.703244 1.685466e-24
XEK.7 12 145 206.481676 206.481676 -86.963353 4.282887e-25 *
KP.2.3 4440 148 200.201152 196.479239 -66.958479 1.944428e-29
|||||

KP.2.6.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.6.2 26 146 7.729416 NaN NaN NaN * * *
GR.1 120 146 7.614753 7.614753 -9.229507 0.891366 * *
HP.1.1 48 146 7.441734 7.441734 -8.883468 0.748264 * *
XBB.1.5.62 311 146 7.154875 7.154875 -8.309750 0.562705 * *
BF.12 89 146 7.111513 7.111513 -8.223025 0.537944 * *
MC.17.1 10 146 6.813126 6.813126 -7.626251 0.400517 * *
XBB.1.44 23 146 5.967853 5.967853 -5.935706 0.172045 * *
XBB.1.17.1 134 146 5.825441 5.825441 -5.650883 0.148823 * *
ED.2 223 146 5.694784 5.694784 -5.389568 0.130680 * *
HU.1.1 72 146 5.556207 5.556207 -5.112413 0.113608 * *



Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2338_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5701_T|C, 6183_A|G, 6636_C|T, 7113_C|T, 7119_C|T, 7842_A|G, 7843_C|T,
8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 14730_G|A, 15714_C|T, 15756_T|A, 16662_G|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21739_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29095_C|T, 29510_A|C, 29734_29759

Case 63 (XEK): USA/IL-CDC-LC1134516/2025


Target: 289 samples Number of changes: 152
BC: XEK.6 + XEC.2 BC BR: 17-18 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-14,19-152Gap history (edge excluded): 14-19
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.42e-29 Rec. model vs L2: 2.46e-29
Flags: Model_2BP_Bad_L1_opp

XEK.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.6 23 14 17.392398 NaN NaN NaN * * *
XEK.7 12 14 17.349839 0.959630 40.080740 9.607894e-01 * *
XEK.2 67 14 17.292601 0.902392 40.195217 9.048374e-01 * *
XEK.1 88 10 16.730292 -7.190950 56.381899 2.774139e-04 *
XEK.1.2 33 10 16.646411 -7.263402 56.526805 2.573689e-04 *
KP.3.1 1957 13 16.423531 -9.968212 61.936424 1.721034e-05 * *
JN.1 17255 13 13.697315 -0.159116 42.318232 3.134862e-01 * *
XEK.5 28 14 9.232507 -7.157702 56.315405 2.858624e-04 * *
XEK.1.1 11 10 8.561713 -15.348101 72.696201 7.930220e-08
BA.5.2.18 582 4 5.301905 -84.479317 210.958634 7.525020e-38
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 19 249.213712 NaN NaN NaN * * *
XEC.18 165 21 247.097740 217.097740 -138.195480 2.486437e-10
XEC.2.3 28 33 233.902806 190.959735 -85.919470 1.104383e-21
XEC.8 592 33 233.600505 218.908493 -141.816985 1.519325e-09
XEK.1 88 20 229.281364 209.281364 -122.562728 9.986072e-14 *
XEK.5 28 20 228.934746 208.934746 -121.869492 7.072339e-14 *
XEK.1.2 33 20 227.770867 199.342314 -102.684629 4.814016e-18 *
XEC.11.1 166 21 223.020012 183.873438 -71.746875 9.250035e-25
XEC.33 169 33 223.000437 192.002090 -88.004180 3.124540e-21
KP.3.3 1715 20 222.303587 214.525076 -133.050152 1.893517e-11 *



Target sequence

, 241_C|T, 248_G|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3505_C|T, 3565_T|C, 3736_C|T, 4184_G|A, 4321_C|T, 5701_T|C, 5761_G|A, 5920_T|C, 6183_A|G, 6601_A|G, 6781_C|T,
7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10969_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19287_T|A, 19716_C|T, 19955_C|T, 20055_A|G, 20262_A|G, 21302_C|T, 21304_C|A,
21305_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C,
22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C,
23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 63 (XEK): USA/NY-PRL-250415_83G08/2025


Target: 289 samples Number of changes: 149
BC: XEK.6 + KP.3.3.10 + XEK.6BC BR: 3-4, 8-9 BC BR coord: 672 - 673, 3430 - 3431
Direction L1: << Initial region span: 1-3,5-8,9-149Gap history (edge excluded): 3-9 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.89e-08
Rec. model vs L1: 8.01e-08 Rec. model vs L2: 9.53e-79
Flags: Model_2BP_Best

XEK.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.6 23 3 7.058661 None None None * * *
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 5 11.104350 NaN NaN NaN * * *
B.1.493 13 7 7.591531 -25.885472 73.770943 1.898418e-12
JG.2 72 6 5.844423 -25.374283 72.748565 3.161419e-12 *
CP.5 75 6 5.817588 -17.193333 56.386666 1.128265e-08 *
AY.104 28 7 5.725663 -30.003001 82.006002 3.083889e-14
JN.1 17255 4 5.427866 5.427866 11.144269 7.556551e+01 * *
N.5 93 7 5.218415 -24.781585 71.563169 5.731751e-12
EG.2 163 6 5.035172 -14.964828 51.929657 1.049271e-07 *
JN.1.4 8971 5 4.643715 -1.330014 24.660027 8.759775e-02 * *
AY.43.2 141 8 4.105222 -25.941812 73.883625 1.796825e-12
|||||

XEK.6 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.6 23 9 237.473449 NaN NaN NaN * * *
XEK.1 88 15 235.494901 241.448869 -168.897738 4.595926e-02 *
XEK.5 28 9 234.567373 241.670486 -169.340971 5.726876e-02 * *
XEC.9 305 22 220.499829 187.240374 -60.480747 1.316040e-25
XEK.2 67 9 219.210596 226.313709 -138.627417 1.228361e-08 *
XEK.1.2 33 15 214.099349 219.969435 -125.938871 2.156391e-11
KP.3.3 1715 16 213.351318 203.284283 -92.568566 1.223275e-18
XEK.1.1 11 15 213.350667 219.220754 -124.441508 1.018607e-11
XEC.2 921 16 209.533185 181.313082 -48.626163 3.516206e-28
XEC.29 135 22 208.604975 157.710619 -1.421239 1.970394e-38



Target sequence

, 241_C|T, 593_C|T, 670_T|G, 829_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3048_A|G, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5392_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16954_C|T, 17285_C|T, 17410_C|T, 18163_A|G, 18171_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19080_A|G, 19716_C|T, 19955_C|T, 20055_A|G, 21077_C|T, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21742_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27481_C|T, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 63 (XEK): IGS-10285-CVDP-5E07523F-5968-4EAF-99D3-0FF692B7D24D


Target: 289 samples Number of changes: 144
BC: XEK.5 + B.1.1.434 + XEK.5BC BR: 5-6, 8-9 BC BR coord: 2792 - 2793, 3430 - 3431
Direction L1: << Initial region span: 1-5,6-8,9-144Gap history (edge excluded): 5-9 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.85e-08
Rec. model vs L1: 1.47e-14 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEK.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.5 28 5 3.603332 None None None * * *
|||||

B.1.1.434 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
B.1.1.434 1274 6 8.009487 NaN NaN NaN * * *
XBB.2.3.14 18 7 6.536776 -3.463224 12.926449 0.000010 * *
B.1.1.304 143 7 6.536776 -3.463224 12.926449 0.000010 * *
AZ.5 21 7 6.536776 -3.463224 12.926449 0.000010 * *
KP.3.1.5 45 7 6.536776 -3.463224 12.926449 0.000010 * *
NL.11 57 7 6.131310 -3.868690 13.737379 0.000007 *
KP.3.1 1957 6 5.331302 5.331302 -4.662603 0.068563 * *
B.1.1.306 97 8 4.523128 -5.493820 16.987640 0.000001
JE.1.1.1 46 7 4.499894 -5.500106 17.000213 0.000001 *
XBB.1.5.77 308 6 4.394709 4.394709 -2.789418 0.026917 * *
|||||

XEK.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.5 28 9 287.216513 NaN NaN NaN * * *
XEK.1 88 15 280.497542 291.156073 -274.312145 1.397940e+00 *
XEK.6 23 9 276.969235 288.732459 -269.464917 1.236871e-01 * *
XEK.2 67 1 275.976074 283.643991 -259.287982 7.654857e-04 *
XEK.1.2 33 15 270.672104 281.246753 -254.493507 6.944330e-05 *
XEK.1.1 11 15 266.017825 276.497165 -244.994329 6.008022e-07
XEC.2 921 16 262.221896 238.686638 -169.373276 2.280642e-23
KP.3.3 1715 16 260.095641 254.704244 -201.408487 2.067544e-16
XEC.2.1 265 27 257.006081 223.302575 -138.605150 4.770985e-30
XEC.8 592 16 254.346062 250.548209 -193.096417 3.243107e-18



Target sequence

, 241_C|T, 593_C|T, 670_T|G, 897_C|A, 2790_C|T, 2947_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3505_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 4780_C|T, 5701_T|C, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9286_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
14556_T|C, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23621_G|A, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 71 (XFB): Denmark/DCGC-692189/2025


Target: 9 samples Number of changes: 148
BC: KP.2.3 + XFB.3 BC BR: 15-16 BC BR coord: 7118 - 7119
Direction L1: << Initial region span: 1-15,17-148Gap history (edge excluded): 15-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.21e-01
Rec. model vs L1: 2.16e-54Rec. model vs L2: 1.73e-13
Flags: Model_1BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 15 27.676390 NaN NaN NaN * * *
MF.1 35 12 27.284261 -11.627622 67.255245 8.512466e-18
KP.3.1.1 12013 15 26.134250 26.134250 -8.268500 2.143811e-01 * *
MC.9 298 12 25.342468 23.335709 -2.671418 1.303653e-02 *
LF.7.9.3 20 10 20.996396 -10.469164 64.938327 2.715420e-17
XFB.3 56 10 20.989870 3.921235 36.157530 4.823192e-11
BA.2.86.1 1343 14 20.007899 10.007899 23.984202 2.129060e-08 *
JN.1.7.6 67 10 19.957551 -14.302615 72.605230 5.865670e-19
JN.1.65.1 46 10 19.947679 -27.922911 99.845822 7.132254e-25
KP.2.8 51 10 19.758085 -0.893584 45.787167 3.910269e-13
|||||

XFB.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFB.3 56 17 246.995466 NaN NaN NaN * * *
KP.3.1.1 12013 1 233.622447 207.488197 -126.976394 1.535116e-13
MC.1 932 1 222.716027 209.045941 -130.091882 7.268909e-13
MC.24 831 14 212.260699 204.266507 -120.533013 6.102975e-15
MC.19 221 17 197.642832 187.642832 -87.285664 3.694599e-22 *
MC.28 304 1 196.599073 181.315025 -74.630050 6.583900e-25
KP.3.1 1957 1 191.675662 177.025984 -66.051968 9.023186e-27
MC.21.1 187 17 188.103654 178.103654 -68.207308 2.657039e-26 *
MC.10.1 650 17 180.678112 170.678112 -53.356224 1.584023e-29 *
MC.42 84 1 180.300534 164.720658 -41.441316 4.086639e-32



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4218_G|A, 4321_C|T, 6040_C|T, 6183_A|G, 7113_C|T, 7471_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C, 14408_C|T,
15372_G|T, 15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19722_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T, 22131_G|C, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22858_C|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24022_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25595_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26690_G|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27752_C|T,
27807_C|T, 27810_T|C, 28211_A|G, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 71 (XFB): OZ285853


Target: 9 samples Number of changes: 151
BC: KP.3.1.1 + LF.7.1.8 + KP.3.1.1BC BR: 138-139, 141-142 BC BR coord: 27387 - 27388, 27810 - 27811
Direction L1: >> Initial region span: 1-138,139-141,144-151Gap history (edge excluded): 138-144 -> 141-144
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.23e-01
Rec. model vs L1: 1.26e-07 Rec. model vs L2: 1.67e-189
Flags: Model_2BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 138 234.570858 NaN NaN NaN * * *
MC.1 932 138 208.439599 206.724207 -95.448413 1.500834e-12 *
XFB.3 56 150 207.845939 213.242383 -108.484765 1.013354e-09
KP.3.1 1957 138 194.065974 181.491795 -44.983591 1.647826e-23 *
MC.24 831 138 192.056902 179.435778 -40.871556 2.110748e-24 *
MC.13 807 138 185.570478 172.981527 -27.963053 3.319445e-27 *
MC.10 221 138 183.579011 171.028903 -24.057806 4.722709e-28 *
MC.19 221 138 181.928622 169.357382 -20.714764 8.846020e-29 *
KP.2.3 4440 138 180.476340 179.277858 -40.555715 1.807676e-24 *
MC.10.1 650 138 179.499675 167.005837 -16.011673 8.436376e-30 *
|||||

LF.7.1.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.1.8 44 141 10.292769 NaN NaN NaN * * *
XEC.3 29 141 10.039505 10.039505 -10.079011 7.749165e-01 * *
XBF.7.1 13 140 9.792451 -0.207549 10.415099 2.739911e-05 * *
XFG.2 500 141 9.590088 9.590088 -9.180177 4.941086e-01 * *
MC.23 64 141 9.247918 9.247918 -8.495836 3.516918e-01 * *
JN.1.29 69 141 9.172695 9.172695 -8.345390 3.262798e-01 * *
KP.3.3.3 288 141 7.743841 7.743841 -5.487682 7.808167e-02 * *
AY.34.2 258 139 6.420271 -15.653220 41.306439 5.371038e-12
KP.2.2 1334 141 6.210864 6.210864 -2.421728 1.682314e-02 * *
BA.2.75.4 36 140 6.208932 -3.791068 17.582136 7.637693e-07 *
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 144 7.419819 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1758_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5672_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 8809_C|T, 9344_C|T, 9424_A|G,
9534_C|T, 9565_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12043_C|T, 12235_A|C, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C,
14408_C|T, 15372_G|T, 15714_C|T, 15756_T|A, 17334_G|T, 17410_C|T, 18163_A|G, 18449_G|T, 18492_A|G, 18894_C|T, 19722_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21633_21641, 21653_21655, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22111_G|T, 22131_G|C, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22666_A|G, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22858_C|T, 22865_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25595_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27546_T|C, 27807_C|T, 27810_T|C, 27982_C|T, 28211_A|G, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): BHR/25000004638/2025


Target: 5350 samples Number of changes: 146
BC: XEC.8 + XEC.2 BC BR: 13-14 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-13,17-146Gap history (edge excluded): 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.12e-02
Rec. model vs L1: 1.13e-21Rec. model vs L2: 5.71e-18
Flags: Model_1BP_Best

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 13 27.259665 NaN NaN NaN * * *
XEC.4.1 68 13 16.558685 16.558685 -7.117369 2.254494e-05 * *
XEC.5 126 13 15.907539 15.907539 -5.815079 1.176949e-05 * *
XEC.39 155 13 15.705718 15.705718 -5.411435 9.587983e-06 *
XEC.32 42 15 14.250469 5.079158 15.841683 2.329960e-10
MC.10.1 650 14 14.198579 8.716119 8.567761 8.830979e-09 *
KP.3.1.1 12013 13 13.612549 13.612549 -1.225098 1.185910e-06 *
LY.1 178 13 11.356933 11.356933 3.286133 1.237503e-07 *
MC.24 831 13 9.510400 9.510400 6.979199 1.955568e-08 *
KP.3.3 1715 13 8.726622 8.726622 8.546756 8.919731e-09 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 232.121365 NaN NaN NaN * * *
XEK.5 28 17 231.627599 197.240788 -106.481577 7.597014e-03 * *
XEC.29 135 17 224.351842 185.788764 -83.577528 8.090421e-08 *
XEC.32 42 7 219.374555 205.300617 -122.601234 2.404675e+01 *
XEC.18 165 17 216.686713 186.686713 -85.373427 1.979998e-07 *
XEC.39 155 17 215.163625 185.163625 -82.327250 4.330490e-08 *
XEC.30 135 17 213.027734 197.021805 -106.043609 6.096747e-03 * *
XEC.2.2 273 17 212.493655 182.493655 -76.987309 2.998961e-09 *
XEC.31 66 17 211.301202 181.301202 -74.602404 9.077973e-10 *
XEC.3 29 17 211.142481 181.142481 -74.284963 7.735738e-10 *



Target sequence

, 241_C|T, 670_T|G, 745_C|T, 897_C|A, 2060_G|A, 2659_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6362_G|A, 7318_C|T, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15162_A|G, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18186_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22893_A|C, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28851_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29762_C|T

Case 72 (XEC): BHR/25020232316/2025


Target: 5350 samples Number of changes: 149
BC: XEC.2 + XEC.25 + XEC.2BC BR: 4-5, 13-14 BC BR coord: 1884 - 1885, 6183 - 6184
Direction L1: << Initial region span: 1-4,5-13,15-149Gap history (edge excluded): 4-15 -> 13-15
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.64e-04
Rec. model vs L1: 9.75e-26Rec. model vs L2: 4.14e-39
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 4 4.959443 None None None * * *
|||||

XEC.25 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.25 13 13 28.661750 NaN NaN NaN * * *
XEC.8.1 12 14 15.688113 10.273328 3.453344 1.036325e-08 *
XEC.24.1 18 9 14.603690 10.303181 3.393638 1.067886e-08
XEC.19 59 9 14.603690 3.572575 16.854850 1.275625e-11
XEC.34 22 9 14.603690 10.360339 3.279322 1.128265e-08
XEC.11.1 166 9 14.603690 1.156036 21.687927 1.134306e-12
XEC.17 13 9 14.603690 10.360339 3.279322 1.128265e-08
XEC.32 42 9 14.603690 10.360339 3.279322 1.128265e-08
XEC.4.6.1 13 9 14.603690 10.360339 3.279322 1.128265e-08
XEC.4.1.4 23 9 14.603690 5.289815 13.420370 7.088233e-11
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 209.885495 NaN NaN NaN * * *
XEC.39 155 32 202.892756 171.031197 -32.062394 2.062206e-15
KP.3.3 1715 42 202.230148 189.193822 -68.387644 1.596950e-07
XEC.2.1 265 42 199.430248 164.960131 -19.920261 4.766116e-18
XEC.4 192 42 192.163249 157.406879 -4.813757 2.494996e-21
XEC.29 135 42 185.229244 165.987965 -21.975931 1.335020e-17
KP.3.1.1 12013 47 180.607989 177.888882 -45.777763 1.966040e-12
XEC.18 165 42 179.195020 154.932544 0.134911 2.110388e-22
XEC.31 66 42 173.452251 138.686316 32.627369 1.849597e-29
XEC.40 52 42 173.440951 132.341371 45.317258 3.246972e-32



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1884_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3971_G|A, 4184_G|A, 4321_C|T, 6183_A|G, 7420_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10733_C|T, 11042_G|T, 11074_C|T, 11288_11296, 11727_G|A, 12043_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15105_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18151_T|C, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 19964_T|C, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25629_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28453_C|T, 28674_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29733_29758, 29759_G|T

Case 72 (XEC): BHR/25040003778/2025


Target: 5350 samples Number of changes: 144
BC: NM.1 + XEC.13 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,7-144Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.03e-212Rec. model vs L2: 6.04e-09
Flags: Model_2BP_Bad_L1_opp

NM.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NM.1 41 4 10.513390 NaN NaN NaN * * *
JN.1.1.7 17 4 8.449310 8.449310 -8.898619 0.126818 * *
MK.2 15 4 7.881326 7.881326 -7.762651 0.071719 * *
MC.9.1 15 4 7.881326 7.881326 -7.762651 0.071719 * *
PA.1.4 14 4 7.876211 7.876211 -7.752421 0.071361 * *
JN.2.2 16 4 7.816787 7.816787 -7.633574 0.067206 * *
MC.5 19 4 7.644937 7.644937 -7.289874 0.056699 * *
JN.1.56 21 4 7.496063 7.496063 -6.992126 0.048801 * *
LF.7.1.3 24 4 7.368762 7.368762 -6.737525 0.043067 * *
KP.4.2 75 4 7.302649 7.302649 -6.605299 0.040357 * *
|||||

XEC.13 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.13 30 7 265.469966 NaN NaN NaN * * *
XEC.2 921 14 261.124216 233.725098 -169.450196 6.710049e-13
XEC.16 23 7 256.091262 252.377663 -206.755326 8.481824e-05 * *
XEC.31 66 14 245.788644 234.600906 -171.201813 1.609657e-12
MC.24.1 25 7 245.783893 241.416368 -184.832735 1.467068e-09 *
XEC.39 155 7 237.583806 233.863734 -169.727469 7.718393e-13 *
KP.3.3 1715 15 236.907737 228.296675 -158.593350 2.941079e-15
XEC.9 305 15 235.877310 230.107992 -162.215984 1.806139e-14
XEC.14 193 3 232.297944 228.083666 -158.167331 2.383992e-15
XEC.28 39 14 231.637429 221.387462 -144.774924 2.934484e-18



Target sequence

, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 2060_G|A, 2286_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13821_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 15849_T|C,
17410_C|T, 18163_A|G, 18315_G|A, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27101_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): Denmark/DCGC-692047/2025


Target: 5350 samples Number of changes: 145
BC: XEC.25 + XEC.2 BC BR: 9-10 BC BR coord: 3566 - 3567
Direction L1: << Initial region span: 1-9,16-145Gap history (edge excluded): 9-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.55e-01
Rec. model vs L1: 3.54e-25Rec. model vs L2: 4.61e-17
Flags: Model_1BP_Best

XEC.25 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.25 13 9 24.715389 NaN NaN NaN * * *
XEC.4 192 9 20.865923 20.865923 -21.731845 2.127974e-02 * *
XEC.9 305 9 20.381513 20.381513 -20.763027 1.310187e-02 * *
XEC.8 592 9 20.371099 20.371099 -20.742198 1.297151e-02 * *
KP.3.3 1715 12 15.994590 14.104611 -8.209223 2.466809e-05 *
KP.3.1 1957 12 15.459081 12.316639 -4.633278 4.118589e-06
MC.24 831 12 15.277126 13.356415 -6.712830 1.165238e-05 *
XEC.39 155 12 13.565774 9.270302 1.459396 1.960296e-07
KP.3.1.12 39 4 11.473441 0.462399 19.075202 2.925414e-11
KP.3.1.1 12013 12 11.384515 9.735863 0.528274 3.120820e-07
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 253.679803 NaN NaN NaN * * *
XEC.9 305 1 225.983668 205.602154 -113.204308 1.761245e-12
KP.3.3 1715 16 225.823976 206.945150 -115.890299 6.759988e-12 *
XEK.5 28 31 222.445529 182.314188 -66.628377 1.359167e-22
XEC.32 42 16 220.030730 195.787379 -93.574758 9.620984e-17 *
XEC.38 34 16 219.996578 195.753227 -93.506455 9.336641e-17 *
XEC.33 169 31 219.238350 190.658688 -83.317375 5.720846e-19
XEC.16 23 16 218.994518 194.751167 -91.502335 3.417627e-17 *
XEC.39 155 5 218.684899 204.120471 -110.240942 4.009258e-13
XEK.1 88 16 217.360017 171.978279 -45.956558 4.414072e-27 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 5518_G|A, 6183_A|G, 6317_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11962_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14055_G|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25665_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29167_C|T, 29510_A|C, 29734_29759, 29769_C|T

Case 72 (XEC): Denmark/DCGC-692052/2025


Target: 5350 samples Number of changes: 143
BC: XEC.24 + JN.1 + XEC.24BC BR: 4-5, 15-16 BC BR coord: 2060 - 2061, 5620 - 5621
Direction L1: << Initial region span: 1-4,5-13,16-143Gap history (edge excluded): 4-16 -> 13-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.81e-17
Rec. model vs L1: 8.65e-26Rec. model vs L2: 1.59e-48
Flags: Model_2BP_Best

XEC.24 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.24 11 4 11.00522 None None None * * *
|||||

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 13 15.465153 NaN NaN NaN * * *
LF.7.1.2 26 5 7.175400 -28.584526 95.169053 6.197319e-19
KP.3.1.1 12013 9 7.019484 0.224152 37.551696 2.014781e-06
BA.5.2.6 3344 5 5.409616 -32.560673 103.121345 1.163813e-20
DF.1 256 5 4.888319 -48.472106 134.944212 1.433039e-27
BQ.1.1.8 1026 5 4.598685 -50.153869 138.307737 2.657491e-28
BA.5.1.23 4202 8 4.448381 -18.040685 74.081369 2.354177e-14
XFG.3 480 5 4.259710 -39.431978 116.863956 1.208593e-23
AY.47 22935 5 4.030663 -68.675780 175.351559 2.406235e-36
B.1.577 618 5 4.007008 -74.434966 186.869931 7.582315e-39
|||||

XEC.24 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.24 11 16 256.811319 NaN NaN NaN * * *
XEC.18 165 16 250.257031 261.244014 -246.488029 1.401797e-03 * *
XEC.6 45 16 249.390178 260.372925 -244.745850 5.872852e-04 * *
XEC.17 13 16 247.601456 258.606676 -241.213352 1.000340e-04 * *
XEC.31 66 16 244.931072 255.905758 -235.811516 6.722839e-06 *
XEC.28 39 16 244.226999 255.153600 -234.307200 3.175644e-06 *
XEC.14 193 16 244.192137 255.171219 -234.342438 3.223638e-06 *
XEC.2 921 16 244.140724 238.822282 -201.644565 2.556416e-13 *
XEC.19 59 16 243.976078 254.929112 -233.858224 2.535804e-06 *
XEC.36 30 16 242.546123 253.551344 -231.102687 6.379538e-07 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2139_A|G, 2589_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3506_A|G, 3565_T|C, 4184_G|A, 4321_C|T, 4891_C|T, 5619_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14790_C|A, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24760_T|C, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28744_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): Denmark/DCGC-692055/2025


Target: 5350 samples Number of changes: 147
BC: XEC.2 + XEC.25 + XEC.2BC BR: 5-6, 11-12 BC BR coord: 896 - 897, 3566 - 3567
Direction L1: << Initial region span: 1-5,6-11,18-147Gap history (edge excluded): 5-18 -> 11-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.25e-01
Rec. model vs L1: 4.80e-17Rec. model vs L2: 5.43e-26
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 5 8.393377 None None None * * *
|||||

XEC.25 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.25 13 11 19.996570 NaN NaN NaN * * *
XEC.4 192 11 16.162852 16.162852 -18.325703 2.170962e-02 * *
XEC.8 592 11 15.721092 15.721092 -17.442183 1.391205e-02 * *
XEC.9 305 11 15.699037 15.699037 -17.398074 1.363657e-02 * *
KP.3.3 1715 14 11.314662 9.424684 -4.849367 2.567482e-05 *
KP.3.1 1957 14 10.777917 7.635475 -1.270950 4.286672e-06
MC.24 831 14 10.584958 8.664247 -3.328494 1.200725e-05 *
XEC.39 155 14 8.859900 4.564428 4.871144 1.989922e-07
JD.1.1.5 61 6 6.859216 -22.059689 58.119379 5.441837e-19
KP.3.1.12 39 6 6.806573 -4.204469 22.408939 3.090819e-11
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 253.050390 NaN NaN NaN * * *
XEC.9 305 1 229.442273 213.743236 -119.486472 2.575442e-12
KP.3.3 1715 18 225.081448 215.514144 -123.028288 1.512004e-11 *
XEK.5 28 33 221.657914 191.452515 -74.905030 5.375610e-22
XEC.38 34 18 219.454357 204.687530 -101.375061 3.008259e-16 *
XEC.32 42 18 219.370547 201.831408 -95.662816 1.722793e-17 *
XEC.33 169 33 218.603237 198.156206 -88.312412 4.367177e-19
XEC.16 23 18 218.223071 200.971993 -93.943986 7.290205e-18 *
XEC.39 155 7 218.013879 211.429158 -114.858316 2.543666e-13
XEC.36 30 16 216.813606 207.841698 -107.683396 7.020093e-15



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 5518_G|A, 6183_A|G, 6317_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11962_C|T, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14055_G|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25665_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29167_C|T, 29510_A|C, 29734_29759, 29769_C|T

Case 72 (XEC): Denmark/DCGC-692133/2025


Target: 5350 samples Number of changes: 149
BC: LB.1.4.1 + XEC.2 BC BR: 15-16 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-5,16-149Gap history (edge excluded): 5-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.29e-145Rec. model vs L2: 2.36e-07
Flags: Model_2BP_Bad_L1_opp

LB.1.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LB.1.4.1 74 5 9.746843 NaN NaN NaN * * *
JN.1.9 576 5 8.679148 -20.870652 93.741304 5.364643e+02 * *
MC.6 366 5 8.271496 -28.499733 108.999467 2.605397e-01 * *
BA.5.2.48 267 4 7.771518 -68.166895 188.333789 1.547331e-18 *
JN.1.43 317 5 7.698286 -21.859784 95.719568 1.993376e+02 * *
BA.5.2.16 361 4 5.420985 -64.364757 180.729515 6.916754e-17 *
XBB.1.21 24 3 5.414703 -72.054615 196.109231 3.163572e-20
DV.1.1 254 4 4.961095 -85.316881 222.633761 5.513571e-26 *
NM.2 28 5 4.868087 -24.667766 101.335532 1.200112e+01 * *
BF.31 90 4 4.838919 -64.932750 181.865499 3.911600e-17 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 243.378221 NaN NaN NaN * * *
XEC.4 192 17 214.047209 204.047209 -122.094419 8.260885e-18 *
XEC.33 169 17 212.307018 202.307018 -118.614035 1.449954e-18 *
XEC.31 66 17 208.782562 198.782562 -111.565125 4.291781e-20 *
XEC.28 39 17 208.499160 191.524620 -97.049239 3.017586e-23 *
XEC.8 592 14 200.890310 198.745143 -111.490286 4.123498e-20
XEC.2.2 273 16 200.522431 200.522431 -115.044861 2.432980e-19 *
XEC.18 165 17 200.196005 190.196005 -94.392009 7.980829e-24 *
XEC.2.1 265 17 198.341674 188.341674 -90.683347 1.248624e-24 *
XEC.17 13 17 197.601456 187.601456 -89.202911 5.957359e-25 *



Target sequence

, 44_C|T, 180_C|T, 241_C|T, 670_T|G, 897_C|A, 1729_G|T, 2060_G|A, 2374_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4067_G|A, 4184_G|A, 4321_C|T, 4890_C|T, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13452_C|T,
13458_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16474_A|G, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19779_A|G, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25493_C|T, 25584_C|T, 25983_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27370_C|T, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): Denmark/DCGC-692246/2025


Target: 5350 samples Number of changes: 145
BC: KP.3.1.1 + XEC.2 BC BR: 16-17 BC BR coord: 6660 - 6661
Direction L1: << Initial region span: 1-16,17-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.41e-03
Rec. model vs L1: 5.14e-63Rec. model vs L2: 2.55e-24
Flags: Model_1BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 16 20.410738 NaN NaN NaN * * *
XEC.35.1 28 13 17.890032 1.499823 39.000354 6.130436e-09
XEC.23 142 13 17.704623 -3.773639 49.547277 3.137530e-11
XEC.4.7 13 13 17.629701 -7.748836 57.497673 5.892063e-13
XEC.17 13 13 16.675670 0.285461 41.429078 1.818962e-09
XEC.15 127 13 16.658880 12.792759 16.414482 4.930007e-04 *
XEC.4 192 13 16.214163 -0.176046 42.352092 1.148281e-09
XEC.38 34 13 16.166447 -0.223762 42.447523 1.092278e-09
XEC.5 126 13 16.154980 -0.235229 42.470458 1.081410e-09
XEC.29 135 13 16.145763 -14.241346 70.482691 8.947387e-16
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 240.728994 NaN NaN NaN * * *
XEC.18 165 17 235.479842 235.479842 -194.959684 5.247518e-03 * *
XEC.9 305 1 234.887699 222.983003 -169.966006 1.965370e-08
XEC.8 592 17 233.875257 233.875257 -191.750513 1.054172e-03 * *
XEC.24 11 17 233.201528 233.201528 -190.403057 5.367383e-04 * *
KP.3.3 1715 1 232.968479 227.277504 -178.555008 1.441250e-06
XEC.19 59 17 230.227296 230.227296 -184.454592 2.739911e-05 * *
XEC.29 135 17 230.104987 230.104987 -184.209974 2.430083e-05 * *
XEC.32 42 17 226.488887 226.488887 -176.977773 6.541037e-07 *
XEC.4 192 17 225.813698 225.813698 -175.627397 3.330411e-07 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2139_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5619_T|C, 6183_A|G, 6651_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15239_A|G, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18166_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21575_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28090_G|A, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28744_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): Japan/BRL25-0126/2025


Target: 5350 samples Number of changes: 145
BC: KP.3.1.1 + XEC.2 BC BR: 16-17 BC BR coord: 6725 - 6726
Direction L1: << Initial region span: 1-16,17-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.25e-04
Rec. model vs L1: 3.40e-59Rec. model vs L2: 1.51e-36
Flags: Model_1BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 16 13.453707 NaN NaN NaN * * *
KP.3.1.12 39 4 11.473441 -33.806928 103.613855 2.987052e-21
KP.2.3 4440 15 10.689706 9.973545 16.052910 3.080741e-02 * *
XEC.25 13 4 10.111699 -9.527962 55.055924 1.041697e-10
JN.1.68 34 4 8.021822 -27.964864 91.929728 1.026887e-18
KR.1.1 33 4 8.019008 -35.151576 106.303153 7.782457e-22
MM.1 35 4 7.993700 -27.961349 91.922699 1.032034e-18
JN.1.21 60 4 7.466884 -28.459178 92.918356 6.259603e-19
KP.2.3.12 62 4 7.450901 -28.491421 92.982842 6.074604e-19
JN.1.7.5 427 4 7.071349 -28.873509 93.747017 4.133468e-19
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 258.708890 NaN NaN NaN * * *
XEC.14 193 17 234.560626 234.560626 -191.121253 3.249288e-11 *
XEC.2.1 265 32 233.050773 226.790232 -175.580464 1.371893e-14
XEC.25 13 32 231.353103 228.256642 -178.513284 5.936925e-14
XEC.36 30 17 229.431970 229.431970 -180.863940 1.922461e-13 *
XEC.30 135 12 228.578389 215.759121 -153.518241 2.223576e-19
XEC.2.2.1 46 32 227.987263 223.737566 -169.475131 6.497136e-16
XEC.18 165 17 227.715961 227.715961 -177.431922 3.459733e-14 *
XEC.8 592 12 225.968956 215.984782 -153.969565 2.784635e-19
XEC.39 155 17 225.561198 225.561198 -173.122397 4.009940e-15 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 1267_C|T, 2060_G|A, 2790_C|T, 2937_C|T, 3037_C|T, 3431_G|T, 3466_T|C, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6720_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10576_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12488_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16650_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22003_A|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25916_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): Japan/BRL25-0174/2025


Target: 5350 samples Number of changes: 145
BC: XEC.15 + XEL.3 BC BR: 142-143 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-142,143-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.28e-09 Rec. model vs L2: 8.18e-101
Flags: Model_2BP_Bad_L1_opp

XEC.15 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.15 127 142 243.035646 NaN NaN NaN * * *
XEC.18 165 145 239.305318 234.515502 -163.031005 1.994394e-04 *
XEC.6 45 142 236.972112 236.972112 -167.944224 2.322758e-03 * *
XEC.4 192 142 236.239126 236.239126 -166.478253 1.119358e-03 * *
XEC.14 193 142 234.315089 234.315089 -162.630177 1.632872e-04 * *
XEC.39 155 142 234.015280 234.015280 -162.030560 1.209661e-04 * *
XEC.8 592 142 232.155677 232.155677 -158.311355 1.883112e-05 * *
XEC.2 921 145 231.328886 228.827610 -151.655220 6.774026e-07
XEC.36 30 142 227.262810 227.262810 -148.525620 1.416368e-07 *
XEC.38 34 142 226.820595 226.820595 -147.641190 9.076428e-08 *
|||||

XEL.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEL.3 10 143 8.355316 NaN NaN NaN * * *
XEL.4 10 143 8.355316 8.355316 -10.710631 1.000000 * *
XEL.5 19 143 8.301248 8.301248 -10.602497 0.946485 * *
LL.1 45 143 8.212215 8.212215 -10.424429 0.865022 * *
BA.3 31 143 8.082593 8.082593 -10.165185 0.763379 * *
JN.1.4.2 736 143 8.047264 8.047264 -10.094527 0.733447 * *
BA.3.1 40 143 7.924533 7.924533 -9.849065 0.650509 * *
XBB.1.5.54 21 143 7.795700 7.795700 -9.591400 0.571209 * *
FL.14 29 143 7.660979 7.660979 -9.321957 0.499074 * *
BE.5 231 143 7.550774 7.550774 -9.101548 0.447088 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3430_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11956_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16332_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18804_C|T, 18894_C|T, 18962_C|A, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26176_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28009_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29311_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): OZ247414


Target: 5350 samples Number of changes: 143
BC: XEC.36 + XEC.14 BC BR: 5-6 BC BR coord: 1472 - 1473
Direction L1: << Initial region span: 1-5,6-143Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.02e-01
Rec. model vs L1: 2.37e-15Rec. model vs L2: 1.55e-17
Flags: Model_1BP_Best

XEC.36 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.36 30 5 12.056909 NaN NaN NaN * * *
KP.4.2.4 22 5 10.642513 10.642513 -11.285026 0.244143 * *
KP.4 35 5 9.713902 9.713902 -9.427804 0.096328 * *
XEC.31 66 5 8.884757 8.884757 -7.769514 0.042004 * *
LF.1.1.1 109 5 8.657713 8.657713 -7.315425 0.033541 * *
KP.3.2.1 70 5 8.495540 8.495540 -6.991080 0.028439 * *
LB.1.8 114 5 8.399290 8.399290 -6.798581 0.025861 * *
KW.1.1 127 5 8.282270 8.282270 -6.564540 0.022937 * *
JN.1.53 62 5 8.043243 8.043243 -6.086486 0.018133 * *
MC.10 221 5 7.961161 7.961161 -5.922322 0.016656 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 6 246.955256 NaN NaN NaN * * *
XEC.25 13 6 246.630563 246.630563 -187.261126 7.225274e-01 * *
XEC.33 169 6 238.915123 238.915123 -171.830246 3.223090e-04 * *
XEC.36 30 1 238.541006 226.484097 -146.968194 1.288226e-09
XEC.18 165 6 238.396306 238.396306 -170.792612 1.916193e-04 * *
XEC.39 155 6 236.968445 236.968445 -167.936890 4.608606e-05 * *
KP.3.3 1715 1 236.200410 231.098196 -156.196392 1.300951e-07
XEC.15 127 6 236.172759 236.172759 -166.345517 2.081160e-05 * *
XEC.29 135 6 234.936926 234.936926 -163.873852 6.022549e-06 *
XEC.5 126 6 233.940272 233.940272 -161.880545 2.226677e-06 *



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1471_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14119_C|T, 14408_C|T, 15267_A|G, 15668_A|C, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22002_A|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26151_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27792_27793, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ247419


Target: 5350 samples Number of changes: 147
BC: XFB.3 + XEC.18 BC BR: 6-7 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-6,10-147Gap history (edge excluded): 6-10
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.01e-208Rec. model vs L2: 8.23e-09
Flags: Model_2BP_Bad_L1_opp

XFB.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFB.3 56 6 13.391693 NaN NaN NaN * * *
KP.2.28.1 10 6 13.318834 13.318834 -14.637668 0.932394 * *
PG.3 31 6 13.219092 13.219092 -14.438183 0.843665 * *
KS.1.1 52 6 12.128262 12.128262 -12.256524 0.283654 * *
BA.2.86 38 6 11.790418 11.790418 -11.580836 0.201897 * *
MU.1 173 6 11.716817 11.716817 -11.433633 0.187308 * *
KP.3.1.10 51 6 11.585726 11.585726 -11.171452 0.164474 * *
XFG.1 14 6 11.498487 11.498487 -10.996974 0.151072 * *
ML.2 67 6 11.494581 11.494581 -10.989162 0.150318 * *
KP.2.14 169 6 11.461630 11.461630 -10.923260 0.145148 * *
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 10 240.561198 NaN NaN NaN * * *
XEC.2 921 9 236.972216 216.972216 -125.944432 5.170273e-05 * *
XEC.4 192 8 235.278602 225.278602 -142.557204 2.101361e-01 *
KP.3.3 1715 10 229.721022 211.450626 -114.901253 2.071133e-07 *
XEC.14 193 10 229.647497 215.933898 -123.867796 1.836617e-05 * *
XEC.5 126 10 228.135490 214.421891 -120.843782 4.037035e-06 *
XEC.32 42 10 228.130308 214.416709 -120.833417 4.016900e-06 *
XEC.25 13 10 227.591618 213.878019 -119.756038 2.352575e-06 *
XEC.40 52 10 226.203093 204.852785 -101.705569 2.831626e-10 *
XEC.9 305 18 226.158126 210.388808 -112.777615 7.175560e-08



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 1959_C|T, 2060_G|A, 2445_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10171_A|G, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18761_T|C, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20670_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21635_21643, 21711_C|T, 21738_T|C, 21765_21770, 21938_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ247681


Target: 5350 samples Number of changes: 146
BC: XEC.8 + LF.4 BC BR: 143-144 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-143,144-146Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.20e-09 Rec. model vs L2: 2.73e-106
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 143 238.622056 NaN NaN NaN * * *
XEC.9 305 143 231.685222 231.685222 -149.370444 9.731231e-04 * *
XEC.18 165 143 230.691897 230.691897 -147.383793 3.597864e-04 * *
XEC.2 921 143 227.962222 227.962222 -141.924445 2.346501e-05 * *
XEC.5 126 143 223.670048 223.670048 -133.340096 3.215863e-07 *
XEC.6 45 143 223.380486 223.380486 -132.760973 2.406313e-07 *
XEC.14 193 143 221.996638 221.996638 -129.993277 6.023574e-08 *
KP.3.3 1715 143 219.297734 219.297734 -124.595468 4.068465e-09 *
XEC.32 42 143 217.295479 217.295479 -120.590957 5.478607e-10 *
XEC.33 169 143 217.160740 217.160740 -120.321479 4.786746e-10 *
|||||

LF.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.4 38 144 9.420716 NaN NaN NaN * * *
LF.4.1 50 144 9.412908 9.412908 -12.825815 0.995012 * *
LF.9 48 144 7.500702 7.500702 -9.001404 0.146607 * *
CH.1.1.7 39 144 7.117473 7.117473 -8.234946 0.099759 * *
PF.1 19 144 6.476277 6.476277 -6.952554 0.052602 * *
MC.1.3 51 144 5.439773 5.439773 -4.879546 0.018686 * *
BA.5.2.37 108 144 4.587857 4.587857 -3.175715 0.007987 * *
XBB.1.5.4 683 144 4.155477 4.155477 -2.310954 0.005169 * *
LB.1.2 199 144 3.950768 3.950768 -1.901537 0.004211 * *
XBB.1.5.17 1117 144 3.439656 3.439656 -0.879311 0.002529 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ247716


Target: 5350 samples Number of changes: 147
BC: XEC.30 + XEC.2 BC BR: 17-18 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-15,21-147Gap history (edge excluded): 15-21
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 8.48e-01
Rec. model vs L1: 3.41e-20Rec. model vs L2: 2.42e-19
Flags: Model_1BP_Best

XEC.30 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.30 135 15 21.876803 NaN NaN NaN * * *
KP.3.3 1715 19 21.168534 15.731465 10.537071 1.284025e+00 *
XEC.35.1 28 13 17.890032 5.102766 31.794468 3.120288e-05 *
XEC.23 142 13 17.704623 -0.170696 42.341391 1.596950e-07
XEC.4.7 13 13 17.629701 -4.145893 50.291787 2.998961e-09
XEC.17 13 13 16.675670 3.888404 34.223192 9.258208e-06
XEC.15 127 13 16.658880 3.863709 34.272583 9.029622e-06
XEC.4 192 13 16.214163 3.426897 35.146206 5.815406e-06
XEC.38 34 13 16.166447 3.379182 35.241637 5.559513e-06
XEC.5 126 13 16.154980 3.367714 35.264572 5.504195e-06
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 21 246.901961 NaN NaN NaN * * *
XEC.30 135 7 235.757938 218.709128 -165.418257 5.465393e-11
XEC.29 135 21 230.812321 226.249974 -180.499947 1.028494e-07 *
XEK.5 28 21 230.675425 219.714658 -167.429317 1.493095e-10 *
XEC.8 592 21 221.359337 216.796990 -161.593980 8.052810e-12 *
KP.3.3 1715 7 220.898240 204.478298 -136.956595 3.610862e-17
XEC.40 52 21 220.694371 216.112605 -160.225211 4.079690e-12 *
XEC.9 305 21 219.695064 215.132717 -158.265434 1.531153e-12 *
XEC.14 193 21 219.054517 214.492169 -156.984339 8.033387e-13 *
XEC.19 59 21 218.239112 213.676764 -155.353529 3.555893e-13 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1919_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5784_C|T, 6183_A|G, 6238_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
8482_T|C, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12514_G|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24910_T|C, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27005_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28113_A|G, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29614_C|T, 29734_29759

Case 72 (XEC): OZ247800


Target: 5350 samples Number of changes: 143
BC: KP.2.3.10 + XEC.14 BC BR: 6-7 BC BR coord: 1701 - 1702
Direction L1: << Initial region span: 1-6,7-143Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.23e-01
Rec. model vs L1: 5.66e-148Rec. model vs L2: 2.58e-17
Flags: Model_1BP_Best

KP.2.3.10 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.10 10 6 17.073087 NaN NaN NaN * * *
KP.3.2.8 26 6 14.349653 14.349653 -16.699307 6.554620e-02 * *
KP.3.1.9 26 6 13.002580 13.002580 -14.005159 1.707739e-02 * *
JN.1.18 431 6 11.935967 11.935967 -11.871935 5.857690e-03 * *
LF.7.9.3 20 5 11.825673 1.825673 8.348653 2.382370e-07 *
XFB.3 56 5 11.670112 1.670112 8.659776 2.040298e-07 *
XEL.5 19 5 11.593891 1.593891 8.812218 1.892873e-07 *
JN.1.7.2 180 6 11.330096 11.330096 -10.660192 3.198735e-03 * *
LC.1 10 5 11.297148 1.297148 9.405704 1.402275e-07 *
XEC.35.1 28 5 11.252812 1.252812 9.494375 1.347291e-07 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 7 223.925313 NaN NaN NaN * * *
XEC.38 34 7 220.257510 220.257510 -144.515020 2.560417e-02 * *
XEC.4 192 7 219.806277 219.806277 -143.612555 1.624451e-02 * *
XEC.9 305 7 218.566509 218.566509 -141.133019 4.700906e-03 * *
XEC.6 45 7 216.614248 216.614248 -137.228496 6.688171e-04 * *
XEC.8 592 7 216.184348 216.184348 -136.368696 4.350716e-04 * *
XEC.30 135 7 215.540663 215.540663 -135.081326 2.282658e-04 * *
MC.24.1 25 7 214.884070 214.884070 -133.768140 1.185708e-04 * *
XEC.18 165 7 214.665222 214.665222 -133.330443 9.515533e-05 * *
XEC.2 921 13 214.265019 199.631724 -103.263449 2.810707e-11



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1686_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11461_C|T, 11727_G|A, 12394_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16200_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21859_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25538_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27047_G|A, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249457


Target: 5350 samples Number of changes: 136
BC: XEC.32 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,18-136Gap history (edge excluded): 14-18
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.60e-33 Rec. model vs L2: 3.03e-25
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 14 23.490995 NaN NaN NaN * * *
XEC.8.1 12 13 19.955191 18.143349 -0.286697 4.771951e-03 * *
KP.3.1.1 12013 16 19.079354 16.491100 3.017799 9.118820e-04 *
JN.1 17255 17 15.450465 11.922416 12.155168 9.445237e-06
XEC.25 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.18.3 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.16 23 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.4.3 10 12 15.079158 -7.384864 50.769728 3.900838e-14
XEC.17 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.24 11 12 15.079158 8.682101 18.635797 3.699123e-07
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 183.586092 NaN NaN NaN * * *
KP.3.3 1715 3 171.436813 161.767818 -43.535636 1.557521e-07
XEC.8 592 3 165.653783 147.099895 -14.199791 6.627259e-14
XEC.18 165 23 160.038268 138.708116 2.583767 1.505231e-17
XEC.19 59 23 158.923365 137.593213 4.813573 4.935883e-18
XEC.14 193 23 156.439818 135.109667 9.780667 4.112852e-19
XEC.2.2.1 46 21 153.193672 133.112240 13.775519 5.566140e-20
XEC.36 30 23 152.571772 131.241621 17.516757 8.578739e-21
XEC.11 16 23 152.566485 131.236333 17.527333 8.535953e-21
XEC.2.2 273 21 151.947393 131.918804 16.162392 1.693338e-20



Target sequence

, 241_C|T, 295_G|A, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7081_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9733_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18499_T|C, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21711_C|T, 21738_T|C, 21812_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24130_C|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26319_A|G, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29253_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249462


Target: 5350 samples Number of changes: 146
BC: XEC.8 + LF.4 BC BR: 143-144 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-143,144-146Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 9.13e-107
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 143 237.747480 NaN NaN NaN * * *
XEC.18 165 143 234.203584 234.203584 -156.407168 2.901333e-02 * *
XEC.9 305 143 231.050766 231.050766 -150.101532 1.237082e-03 * *
XEC.2 921 143 227.803631 227.803631 -143.607263 4.820730e-05 * *
XEC.11 16 143 225.053248 225.053248 -138.106496 3.081790e-06 *
XEC.19 59 143 223.566694 223.566694 -135.133389 6.945512e-07 *
XEC.6 45 143 223.091103 223.091103 -134.182207 4.319310e-07 *
XEC.5 126 143 222.580647 222.580647 -133.161293 2.593727e-07 *
XEC.32 42 143 222.487319 222.487319 -132.974638 2.358665e-07 *
XEC.14 193 143 221.640518 221.640518 -131.281037 1.013182e-07 *
|||||

LF.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.4 38 144 9.420716 NaN NaN NaN * * *
LF.4.1 50 144 9.412908 9.412908 -12.825815 0.995012 * *
LF.9 48 144 7.500702 7.500702 -9.001404 0.146607 * *
CH.1.1.7 39 144 7.117473 7.117473 -8.234946 0.099759 * *
PF.1 19 144 6.476277 6.476277 -6.952554 0.052602 * *
MC.1.3 51 144 5.439773 5.439773 -4.879546 0.018686 * *
BA.5.2.37 108 144 4.587857 4.587857 -3.175715 0.007987 * *
XBB.1.5.4 683 144 4.155477 4.155477 -2.310954 0.005169 * *
LB.1.2 199 144 3.950768 3.950768 -1.901537 0.004211 * *
XBB.1.5.17 1117 144 3.439656 3.439656 -0.879311 0.002529 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249475


Target: 5350 samples Number of changes: 144
BC: XEC.4.3 + XEC.2 BC BR: 11-12 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-8,12-144Gap history (edge excluded): 8-12
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.61e-06
Rec. model vs L1: 2.67e-45Rec. model vs L2: 1.07e-17
Flags: Model_1BP_Best

XEC.4.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.3 10 8 19.322509 NaN NaN NaN * * *
XEC.25 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.32 42 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.8.1 12 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.18.3 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.4.1.4 23 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.16 23 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.17 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.24 11 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.22 23 8 19.322509 11.469367 -0.938735 1.0 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 12 265.769700 NaN NaN NaN * * *
XEC.2.2 273 12 240.387585 240.387585 -194.775169 9.497429e-12 *
XEC.8 592 1 240.308765 228.961356 -171.922711 1.031858e-16
XEC.33 169 1 236.834593 225.437197 -164.874394 3.039010e-18
KP.3.3 1715 1 236.282739 229.445069 -172.890138 1.675919e-16
XEC.14 193 3 236.121775 225.780481 -165.560963 4.291051e-18
XEC.9 305 1 230.573627 219.187445 -152.374889 5.866669e-21
XEC.31 66 1 225.493343 221.992796 -157.985593 9.744489e-20
XEC.2.1 265 13 224.451157 214.451157 -142.902314 5.152372e-23 *
XEC.15 127 1 222.740260 211.368779 -136.737558 2.367992e-24



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3914_G|A, 4184_G|A, 4321_C|T, 5178_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11866_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17795_C|T,
18084_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20405_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29020_A|G, 29353_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249692


Target: 5350 samples Number of changes: 145
BC: XEC.8 + LF.4 BC BR: 142-143 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-142,143-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 4.09e-106
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 142 241.280891 NaN NaN NaN * * *
XEC.9 305 142 234.806936 234.806936 -159.613871 1.541499e-03 * *
XEC.18 165 142 233.998499 233.998499 -157.996998 6.891856e-04 * *
XEC.2 921 142 231.443793 231.443793 -152.887587 5.354436e-05 * *
XEC.6 45 142 226.502137 226.502137 -143.004274 3.811778e-07 *
XEC.5 126 142 226.202825 226.202825 -142.405649 2.837989e-07 *
XEC.14 193 142 225.194061 225.194061 -140.388122 1.033649e-07 *
XEC.32 42 142 222.757859 222.757859 -135.515719 9.054536e-09 *
KP.3.3 1715 142 221.914177 221.914177 -133.828354 3.889443e-09 *
XEC.33 169 142 220.912909 220.912909 -131.825818 1.430846e-09 *
|||||

LF.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.4 38 143 9.420716 NaN NaN NaN * * *
LF.4.1 50 143 9.412908 9.412908 -12.825815 0.995012 * *
LF.9 48 143 7.500702 7.500702 -9.001404 0.146607 * *
CH.1.1.7 39 143 7.117473 7.117473 -8.234946 0.099759 * *
PF.1 19 143 6.476277 6.476277 -6.952554 0.052602 * *
MC.1.3 51 143 5.439773 5.439773 -4.879546 0.018686 * *
BA.5.2.37 108 143 4.587857 4.587857 -3.175715 0.007987 * *
XBB.1.5.4 683 143 4.155477 4.155477 -2.310954 0.005169 * *
LB.1.2 199 143 3.950768 3.950768 -1.901537 0.004211 * *
XBB.1.5.17 1117 143 3.439656 3.439656 -0.879311 0.002529 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17676_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249699


Target: 5350 samples Number of changes: 135
BC: XEC.32 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,18-135Gap history (edge excluded): 14-18
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.56e-33 Rec. model vs L2: 3.03e-25
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 14 23.490995 NaN NaN NaN * * *
XEC.8.1 12 13 19.955191 18.143349 -0.286697 4.771951e-03 * *
KP.3.1.1 12013 16 19.079354 16.491100 3.017799 9.118820e-04 *
JN.1 17255 17 15.450465 11.922416 12.155168 9.445237e-06
XEC.25 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.18.3 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.16 23 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.4.3 10 12 15.079158 -7.384864 50.769728 3.900838e-14
XEC.17 13 12 15.079158 8.682101 18.635797 3.699123e-07
XEC.24 11 12 15.079158 8.682101 18.635797 3.699123e-07
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 180.051805 NaN NaN NaN * * *
KP.3.3 1715 3 167.916458 158.247464 -36.494927 1.573175e-07
XEC.8 592 3 162.113193 143.559305 -7.118611 6.594205e-14
XEC.18 165 23 156.527608 135.197456 9.605087 1.535639e-17
XEC.19 59 23 155.376006 134.045855 11.908289 4.862398e-18
XEC.14 193 23 152.913293 131.583142 16.833716 4.154187e-19
XEC.2.2.1 46 21 149.690271 129.608840 20.782320 5.764405e-20
XEC.36 30 23 149.162400 127.832249 24.335502 9.720985e-21
XEC.11 16 23 149.019126 127.688975 24.622050 8.451018e-21
XEC.2.2 273 21 148.407374 128.378785 23.242430 1.684893e-20



Target sequence

, 241_C|T, 295_G|A, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7081_C|T, 7842_A|G, 7869_C|T, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9733_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18499_T|C, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21711_C|T, 21738_T|C, 21812_C|A, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24130_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26319_A|G, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29253_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249708


Target: 5350 samples Number of changes: 146
BC: XEC.8 + LF.4 BC BR: 143-144 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-143,144-146Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.17e-09 Rec. model vs L2: 9.89e-107
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 143 237.685831 NaN NaN NaN * * *
XEC.18 165 143 234.195624 234.195624 -156.391248 3.050087e-02 * *
XEC.9 305 143 231.170660 231.170660 -150.341319 1.481056e-03 * *
XEC.2 921 143 227.791937 227.791937 -143.583873 5.042618e-05 * *
XEC.11 16 143 225.357131 225.357131 -138.714262 4.417220e-06 *
XEC.19 59 143 223.550187 223.550187 -135.100374 7.265199e-07 *
XEC.6 45 143 223.208806 223.208806 -134.417611 5.171153e-07 *
XEC.5 126 143 222.598328 222.598328 -133.196656 2.809750e-07 *
XEC.32 42 143 222.505001 222.505001 -133.010001 2.555111e-07 *
XEC.14 193 143 221.669661 221.669661 -131.339323 1.108597e-07 *
|||||

LF.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.4 38 144 9.420716 NaN NaN NaN * * *
LF.4.1 50 144 9.412908 9.412908 -12.825815 0.995012 * *
LF.9 48 144 7.500702 7.500702 -9.001404 0.146607 * *
CH.1.1.7 39 144 7.117473 7.117473 -8.234946 0.099759 * *
PF.1 19 144 6.476277 6.476277 -6.952554 0.052602 * *
MC.1.3 51 144 5.439773 5.439773 -4.879546 0.018686 * *
BA.5.2.37 108 144 4.587857 4.587857 -3.175715 0.007987 * *
XBB.1.5.4 683 144 4.155477 4.155477 -2.310954 0.005169 * *
LB.1.2 199 144 3.950768 3.950768 -1.901537 0.004211 * *
XBB.1.5.17 1117 144 3.439656 3.439656 -0.879311 0.002529 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ249750


Target: 5350 samples Number of changes: 147
BC: XEC.8 + LF.4 BC BR: 144-145 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-144,145-147Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.20e-09 Rec. model vs L2: 3.56e-106
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 144 245.806625 NaN NaN NaN * * *
XEC.9 305 144 238.969082 238.969082 -163.938164 1.075467e-03 * *
XEC.18 165 144 238.014630 238.014630 -162.029260 4.138529e-04 * *
XEC.2 921 144 235.155612 235.155612 -156.311225 2.370084e-05 * *
XEC.5 126 144 230.952438 230.952438 -147.904877 3.536352e-07 *
XEC.6 45 144 230.642080 230.642080 -147.284159 2.593727e-07 *
XEC.14 193 144 229.248604 229.248604 -144.497208 6.460332e-08 *
KP.3.3 1715 144 226.545771 226.545771 -139.091542 4.320045e-09 *
XEC.32 42 144 224.743253 224.743253 -135.486505 7.140986e-10 *
XEC.33 169 144 224.356609 224.356609 -134.713217 4.834854e-10 *
|||||

LF.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.4 38 145 9.420716 NaN NaN NaN * * *
LF.4.1 50 145 9.412908 9.412908 -12.825815 0.995012 * *
LF.9 48 145 7.500702 7.500702 -9.001404 0.146607 * *
CH.1.1.7 39 145 7.117473 7.117473 -8.234946 0.099759 * *
PF.1 19 145 6.476277 6.476277 -6.952554 0.052602 * *
MC.1.3 51 145 5.439773 5.439773 -4.879546 0.018686 * *
BA.5.2.37 108 145 4.587857 4.587857 -3.175715 0.007987 * *
XBB.1.5.4 683 145 4.155477 4.155477 -2.310954 0.005169 * *
LB.1.2 199 145 3.950768 3.950768 -1.901537 0.004211 * *
XBB.1.5.17 1117 145 3.439656 3.439656 -0.879311 0.002529 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3179_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5884_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15240_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 17676_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19018_C|T, 19716_C|T, 19806_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24821_G|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25186_G|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29427_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ252346


Target: 5350 samples Number of changes: 145
BC: KP.3.3 + XEC.30 BC BR: 8-9 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-8,10-145Gap history (edge excluded): 8-10
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.50e-01
Rec. model vs L1: 4.35e-23Rec. model vs L2: 1.08e-10
Flags: Model_1BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 8 13.882190 NaN NaN NaN * * *
XEC.17 13 8 9.973636 9.973636 4.052727 2.014095e-02 * *
JN.1 17255 7 8.909044 -1.090956 26.181912 3.152184e-07 *
KP.3.1.1 12013 7 8.902425 5.795081 12.409837 3.081265e-04 * *
XEC.29 135 8 7.818912 7.818912 8.362177 2.334401e-03 * *
LF.7.9.3 20 3 7.111420 -18.174327 60.348653 1.198644e-14
XFB.3 56 3 6.955858 -18.329888 60.659776 1.026537e-14
NY.12.1 17 3 6.912387 -36.265998 96.531996 1.668412e-22
XEL.5 19 3 6.879637 -29.632125 83.264250 1.270127e-19
MC.13.2.4 37 3 6.742160 -26.379166 76.758332 3.275700e-18
|||||

XEC.30 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.30 135 10 251.173011 NaN NaN NaN * * *
XEC.14 193 10 244.536353 234.536353 -173.072705 1.307027e-03 * *
XEC.2 921 17 244.451479 227.052361 -158.104723 7.338215e-07
XEC.9 305 18 241.134674 229.078955 -162.157909 5.587380e-06
XEC.40 52 10 240.941351 223.304642 -150.609284 1.734433e-08 *
XEC.18 165 10 239.301526 229.301526 -162.603052 6.962305e-06 *
XEC.6 45 10 238.641398 228.641398 -161.282797 3.598476e-06 *
XEC.39 155 10 238.510654 228.510654 -161.021308 3.159806e-06 *
XEC.17 13 5 238.147982 223.385214 -150.770428 1.878889e-08
XEC.31 66 28 237.758381 217.468768 -138.937537 5.070483e-11



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 505_T|C, 670_T|G, 897_C|A, 934_C|T, 2060_G|A, 2504_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6023_T|C, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 9995_T|G, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14123_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27198_A|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ252347


Target: 5350 samples Number of changes: 144
BC: KP.3.3 + XEC.2 BC BR: 16-17 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-16,18-144Gap history (edge excluded): 16-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.36e-05
Rec. model vs L1: 1.51e-17Rec. model vs L2: 5.74e-22
Flags: Model_1BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 16 12.726113 NaN NaN NaN * * *
KP.2.3.2 28 4 10.921530 -14.010545 62.021089 2.449836e-12
JN.1.11 43 4 10.145369 -14.868558 63.737115 1.036678e-12
KP.2.3 4440 7 10.132628 9.468492 15.063016 3.858082e-02 *
LF.7.1 165 4 9.226868 -15.643625 65.287249 4.776014e-13
JN.1.4.5 1757 6 8.072072 -4.415975 42.831951 3.599089e-08
JN.1 17255 7 7.743457 5.044672 23.910656 4.619749e-04 *
LF.7.9.3 20 3 7.111420 -27.933323 89.866646 2.195768e-18
MC.24 831 4 7.069973 2.141111 29.717778 2.529257e-05 *
XFB.3 56 3 6.955858 -27.939849 89.879698 2.184816e-18
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 243.046368 NaN NaN NaN * * *
XEC.4 192 18 232.046389 222.046389 -158.092777 1.670170e-05 * *
XEC.29 135 19 225.501038 205.113930 -124.227859 7.415751e-13 *
KP.3.3 1715 6 225.237159 208.483904 -130.967809 2.156391e-11
XEC.9 305 19 221.541225 209.068200 -132.136401 3.870703e-11 *
XEC.13 30 18 218.276296 208.276296 -130.552592 1.747937e-11 *
XEC.2.2.1 46 18 217.929696 207.929696 -129.859392 1.237924e-11 *
XEC.39 155 6 216.164865 203.719601 -121.439202 1.837868e-13
XEC.8 592 18 215.072311 205.072311 -124.144621 7.089439e-13 *
XEC.14 193 7 214.703812 203.549114 -121.098227 1.550545e-13



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 547_C|T, 616_T|C, 670_T|G, 897_C|A, 936_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3602_C|T, 4184_G|A, 4321_C|T, 5192_C|A, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18131_C|T, 18163_A|G, 18488_T|C, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20451_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25162_C|T, 25207_C|T, 25521_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ252376


Target: 5350 samples Number of changes: 142
BC: XFG.3 + XEC.17 BC BR: 8-9 BC BR coord: 899 - 900
Direction L1: << Initial region span: 1-8,9-142Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.15e-03
Rec. model vs L1: 2.89e-244Rec. model vs L2: 4.34e-11
Flags: Model_1BP_Best

XFG.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFG.3 480 8 14.594840 NaN NaN NaN * * *
KS.1.1.2 252 7 10.984879 0.984879 14.030243 1.228152e-06 *
BA.2.86.1 1343 8 10.710812 10.710812 -5.421625 2.054783e-02 * *
MC.35 258 7 10.586893 0.586893 14.826214 8.232549e-07 *
KP.3.1.4 511 7 10.375968 0.375968 15.248065 6.673174e-07 *
MC.16 917 7 8.838234 -1.161766 18.323532 1.437773e-07 *
XEC.17 13 4 8.775898 -6.509849 29.019697 6.826765e-10
KP.3.1.1 12013 8 8.745007 8.745007 -1.490014 2.879899e-03 * *
JN.1.64.1 14 4 8.594396 -6.999652 29.999304 4.182256e-10
KP.2.2 1334 7 8.324334 -1.675666 19.351332 8.590704e-08 *
|||||

XEC.17 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.17 13 9 236.871490 NaN NaN NaN * * *
XEC.14 193 9 224.706822 224.706822 -155.413644 5.209639e-06 *
XEC.38 34 9 221.024500 221.024500 -148.048999 1.314026e-07 *
XEC.4 192 9 220.545730 220.545730 -147.091460 8.130974e-08 *
XEC.9 305 9 219.306120 219.306120 -144.612240 2.352976e-08 *
XEC.6 45 9 217.413891 217.413891 -140.827781 3.554683e-09 *
XEC.8 592 9 217.052861 217.052861 -140.105722 2.480018e-09 *
XEC.30 135 9 216.454556 216.454556 -138.909111 1.361063e-09 *
MC.24.1 25 9 215.662274 215.662274 -137.324548 6.146304e-10 *
XEC.18 165 9 215.374343 215.374343 -136.748686 4.622108e-10 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 583_C|T, 635_C|T, 670_T|G, 897_C|A, 898_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8664_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17097_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21764_21769, 21770_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27580_27616, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ252580


Target: 5350 samples Number of changes: 136
BC: XEC.4 + XEC.2 BC BR: 13-14 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-11,16-136Gap history (edge excluded): 11-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.72e-35 Rec. model vs L2: 2.21e-24
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 11 19.610508 NaN NaN NaN * * *
XEC.18 165 11 19.042211 12.639075 16.721849 5.627049e-01 * *
XEC.8 592 11 17.718321 11.319573 19.360853 1.503183e-01 * *
KP.3.3 1715 11 12.126020 1.352704 39.294593 7.067526e-06 *
XEC.18.2 10 11 11.417667 5.020611 31.958779 2.760303e-04 * *
XEC.1 99 11 9.617396 3.220339 35.559322 4.562750e-05 * *
KP.3.1 1957 11 8.991071 -1.791261 45.582522 3.043766e-07 *
PY.4 10 4 8.702742 -21.103047 84.206093 1.244553e-15
KP.2.14.1 13 4 8.545738 -20.598457 83.196914 2.062206e-15
JN.1 17255 15 8.256835 4.333642 33.332716 1.391442e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 200.197467 NaN NaN NaN * * *
XEC.8 592 1 183.352989 172.033415 -66.066831 3.690828e-10
XEC.19 59 16 183.286016 176.841610 -75.683220 4.507221e-08 *
KP.3.3 1715 16 180.051973 173.607567 -69.215134 1.782944e-09 *
XEC.30 135 3 177.558874 166.187766 -54.375532 1.068249e-12
XEC.39 155 3 172.777755 161.416302 -44.832604 9.013977e-15
XEC.9 305 16 170.975963 164.531558 -51.063115 2.031158e-13 *
XEC.14 193 4 170.973367 160.710989 -43.421978 4.453883e-15
XEC.2.2.1 46 19 167.697041 157.615610 -37.231220 2.016496e-16
XEC.18 165 1 166.650980 154.011905 -30.023810 5.482338e-18



Target sequence

, 241_C|T, 635_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6406_C|T, 7842_A|G, 8293_C|T, 8299_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14790_C|T, 15126_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20404_C|T, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21812_C|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C,
22813_G|T, 22879_C|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C,
23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28254, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ253886


Target: 5350 samples Number of changes: 148
BC: XEC.11 + XEC.2 BC BR: 16-17 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-12,19-148Gap history (edge excluded): 12-19
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.55e-06
Rec. model vs L1: 3.03e-27Rec. model vs L2: 8.21e-27
Flags: Model_1BP_Best

XEC.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.11 16 12 29.383520 NaN NaN NaN * * *
XEC.11.1 166 12 29.170127 15.722473 6.555054 8.108602e-05 * *
KP.3.3 1715 16 18.687254 18.687254 0.625492 1.572639e-03 *
XEC.11.1.1 12 12 18.317398 4.875786 28.248427 1.581329e-09 *
XEC.35.1 28 12 17.918241 13.674890 10.650221 1.049092e-05 * *
XEC.14 193 12 16.252217 12.008866 13.982268 1.984785e-06 *
XEC.13 30 17 16.162531 10.955762 16.088475 6.910871e-07
XEC.24.1 18 12 15.861852 11.561343 14.877315 1.265555e-06 *
XEC.23 142 12 15.686687 6.355283 25.289433 6.946694e-09 *
XEC.38 34 12 15.577978 11.334627 15.330746 1.010566e-06 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 19 218.384527 NaN NaN NaN * * *
XEC.33 169 52 208.145394 188.073475 -88.146951 4.586401e-07
KP.3.3 1715 19 206.180018 181.803758 -75.607517 8.678519e-10 *
XEC.13 30 7 205.105637 191.151845 -94.303690 9.929504e-06
XEK.5 28 19 204.299162 179.912351 -71.824702 1.304541e-10 *
XEC.2.2 273 19 200.563447 180.563447 -73.126894 2.511427e-10 *
XEC.8 592 19 200.384129 185.805217 -83.610434 4.738311e-08 *
XEC.39 155 19 198.117564 178.117564 -68.235128 2.178063e-11 *
XEC.9 305 19 197.347986 171.265171 -54.530342 2.296052e-14 *
XEC.29 135 19 197.226078 168.663000 -49.326000 1.705360e-15 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_520, 670_T|G, 829_C|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4181_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 6250_C|T, 6402_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14184_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16338_C|T, 17410_C|T, 17856_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19028_A|G, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTNT, 21618_C|T,
21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27579_27581, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): OZ253899


Target: 5350 samples Number of changes: 144
BC: XEC.6 + XEC.2 BC BR: 13-14 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-13,17-144Gap history (edge excluded): 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.80e-33 Rec. model vs L2: 7.20e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 13 26.742494 NaN NaN NaN * * *
PG.3 31 13 26.401080 26.401080 -26.802160 0.711770 * *
XEC.28 39 13 24.665462 24.665462 -23.330925 0.125556 * *
XEC.4 192 15 23.051273 16.214163 -6.428326 0.000027 *
XEC.5 126 15 22.432474 16.154980 -6.309960 0.000025 *
MC.24 831 15 22.393442 18.004705 -10.009410 0.000161 *
KP.3.1 1957 15 21.637916 18.510306 -11.020613 0.000267 *
XEC.25 13 15 20.947831 13.497616 -0.995232 0.000002
XEC.32 42 15 19.732255 13.454761 -0.909521 0.000002
KP.3.1.1 12013 15 19.340654 16.323422 -6.646844 0.000030 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 266.291455 NaN NaN NaN * * *
KP.3.3 1715 4 243.753457 226.915786 -167.831572 1.213825e-15
XEC.9 305 17 234.878537 212.405513 -138.811025 6.060983e-22 *
XEC.2.2 273 24 233.676393 211.916366 -137.832731 3.713118e-22
XEC.18 165 4 231.254683 209.821902 -133.643803 4.569744e-23
XEC.39 155 4 229.918031 208.500871 -131.001741 1.220740e-23
XEC.38 34 4 229.839194 208.460304 -130.920608 1.172874e-23
XEC.6 45 1 228.039001 201.296507 -116.593014 9.068415e-27
XEC.4 192 4 227.712175 206.301116 -126.602231 1.352618e-24
XEC.14 193 6 227.533320 207.192026 -128.384052 3.293801e-24



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ253914


Target: 5350 samples Number of changes: 142
BC: XEC.6 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-10,16-142Gap history (edge excluded): 10-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.13e-33 Rec. model vs L2: 6.85e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 10 21.025611 NaN NaN NaN * * *
PG.3 31 10 20.727304 19.281664 -12.563327 0.759572 * *
XEC.28 39 10 18.857113 17.342480 -8.684961 0.109154 * *
XEC.4 192 14 15.813411 8.976300 8.047400 0.000025 *
MC.24 831 14 15.151503 10.762766 4.474469 0.000152 *
XEC.5 126 14 15.141493 8.863999 8.272003 0.000023 *
KP.3.1 1957 14 14.414457 11.286848 3.426305 0.000256 *
XEC.25 13 14 13.624849 6.174634 13.650732 0.000002
XFB.3 56 6 13.391693 6.606966 12.786068 0.000002
KP.2.28.1 10 6 13.318834 6.459999 13.080002 0.000002
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 262.717046 NaN NaN NaN * * *
XEC.2.2 273 22 233.526708 204.605241 -121.210482 3.244211e-22
XEC.9 305 22 232.585592 205.179474 -122.358947 5.765386e-22
KP.3.3 1715 4 229.224421 219.650556 -151.301113 1.109352e-15
XEC.15 127 25 225.043735 188.942343 -89.884685 5.103710e-29
XEC.18 165 22 224.090972 202.773748 -117.547495 5.204154e-23
XEC.39 155 22 222.729770 201.393521 -114.787043 1.309254e-23
XEC.14 193 22 221.334989 200.011685 -112.023371 3.277373e-24
XEC.38 34 16 221.162256 201.169104 -114.338208 1.045460e-23 *
XEC.2.1 265 25 220.942991 181.215578 -74.431156 2.254037e-32



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28651_C|T, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ253899


Target: 5350 samples Number of changes: 144
BC: XEC.6 + XEC.2 BC BR: 13-14 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-13,17-144Gap history (edge excluded): 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.80e-33 Rec. model vs L2: 7.20e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 13 26.742494 NaN NaN NaN * * *
PG.3 31 13 26.401080 26.401080 -26.802160 0.711770 * *
XEC.28 39 13 24.665462 24.665462 -23.330925 0.125556 * *
XEC.4 192 15 23.051273 16.214163 -6.428326 0.000027 *
XEC.5 126 15 22.432474 16.154980 -6.309960 0.000025 *
MC.24 831 15 22.393442 18.004705 -10.009410 0.000161 *
KP.3.1 1957 15 21.637916 18.510306 -11.020613 0.000267 *
XEC.25 13 15 20.947831 13.497616 -0.995232 0.000002
XEC.32 42 15 19.732255 13.454761 -0.909521 0.000002
KP.3.1.1 12013 15 19.340654 16.323422 -6.646844 0.000030 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 266.291455 NaN NaN NaN * * *
KP.3.3 1715 4 243.753457 226.915786 -167.831572 1.213825e-15
XEC.9 305 17 234.878537 212.405513 -138.811025 6.060983e-22 *
XEC.2.2 273 24 233.676393 211.916366 -137.832731 3.713118e-22
XEC.18 165 4 231.254683 209.821902 -133.643803 4.569744e-23
XEC.39 155 4 229.918031 208.500871 -131.001741 1.220740e-23
XEC.38 34 4 229.839194 208.460304 -130.920608 1.172874e-23
XEC.6 45 1 228.039001 201.296507 -116.593014 9.068415e-27
XEC.4 192 4 227.712175 206.301116 -126.602231 1.352618e-24
XEC.14 193 6 227.533320 207.192026 -128.384052 3.293801e-24



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ253930


Target: 5350 samples Number of changes: 143
BC: XEC.6 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-10,16-143Gap history (edge excluded): 10-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.29e-33 Rec. model vs L2: 6.85e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 10 21.025611 NaN NaN NaN * * *
PG.3 31 10 20.727304 19.281664 -12.563327 0.759572 * *
XEC.28 39 10 18.857113 17.342480 -8.684961 0.109154 * *
XEC.4 192 14 15.813411 8.976300 8.047400 0.000025 *
MC.24 831 14 15.151503 10.762766 4.474469 0.000152 *
XEC.5 126 14 15.141493 8.863999 8.272003 0.000023 *
KP.3.1 1957 14 14.414457 11.286848 3.426305 0.000256 *
XEC.25 13 14 13.624849 6.174634 13.650732 0.000002
XFB.3 56 6 13.391693 6.606966 12.786068 0.000002
KP.2.28.1 10 6 13.318834 6.459999 13.080002 0.000002
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 269.894683 NaN NaN NaN * * *
XEC.2.2 273 22 240.701886 211.780418 -135.560837 3.244211e-22
XEC.9 305 22 239.769711 212.363593 -136.727186 5.823329e-22
KP.3.3 1715 4 236.412347 226.838482 -165.676965 1.126118e-15
XEC.15 127 25 232.241012 196.139620 -104.279240 5.232911e-29
XEC.18 165 22 231.276091 209.958867 -131.917733 5.256457e-23
XEC.39 155 22 229.914102 208.577853 -129.155707 1.322412e-23
XEC.14 193 22 228.532266 207.208963 -126.417925 3.360340e-24
XEC.38 34 16 228.359533 208.366381 -128.732762 1.066580e-23 *
XEC.2.1 265 25 228.117497 188.390085 -88.780169 2.254037e-32



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28651_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ255358


Target: 5350 samples Number of changes: 135
BC: XEC.29 + KP.3.1.1 BC BR: 46-47 BC BR coord: 20059 - 20060
Direction L1: << Initial region span: 1-10,50-135Gap history (edge excluded): 10-50
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.36e-06
Rec. model vs L1: 5.27e-03Rec. model vs L2: 1.14e-53
Flags: Model_1BP_Best

XEC.29 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.29 135 10 25.810025 NaN NaN NaN * * *
JN.1 17255 36 25.121783 14.172950 79.654101 4.242574e-02 *
LB.1.3 778 36 21.308170 -13.504411 135.008821 4.039784e-14
JN.1.13.1 751 36 19.360688 -9.658035 127.316070 1.888950e-12
LB.1 1128 36 18.607672 -1.801574 111.603149 4.895252e-09
XEC.17 13 46 16.950408 16.950408 74.099183 6.804506e-01 *
KP.3.3 1715 36 16.606773 7.137632 93.724735 3.735664e-05 *
XEC.38 34 46 16.591667 16.591667 74.816666 4.747343e-01 *
KP.3.1 1957 34 16.565975 -6.886910 121.773821 3.029616e-11
XEC.5 126 46 16.560985 16.560985 74.878031 4.607038e-01 *
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 50 143.178104 NaN NaN NaN * * *
XEC.17 13 50 134.965102 95.979602 18.040797 1.609109e-08 *
MR.2 14 50 134.332198 96.615330 16.769339 3.036425e-08 *
XEC.15 127 50 131.381088 89.512564 30.974873 2.505369e-11 *
XEC.2 921 40 131.309845 110.462585 -10.925169 3.142976e-02 *
XEK.1.2 33 50 131.302972 94.874388 20.251223 5.329545e-09 *
XEC.2.2 273 50 131.181543 97.722242 14.555517 9.167648e-08 *
XEC.9 305 50 131.139648 97.469838 15.060324 7.139771e-08 *
XEK.5 28 50 131.079532 97.365644 15.268712 6.428111e-08 *
XEC.25 13 50 131.070597 93.759877 22.480245 1.747639e-09 *



Target sequence

, 37_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3682_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10396_G|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12667_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16257_T|C, 17410_C|T, 18116_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20400_A|G, 21738_T|C, 21752_T|A, 21941_G|T, 21987_G|A, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24460_T|C, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26966_T|C, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28913_G|A, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ256652


Target: 5350 samples Number of changes: 145
BC: XEC.6 + XEC.2 BC BR: 13-14 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-13,17-145Gap history (edge excluded): 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.44e-33 Rec. model vs L2: 7.20e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 13 26.742494 NaN NaN NaN * * *
PG.3 31 13 26.401080 26.401080 -26.802160 0.711770 * *
XEC.28 39 13 24.665462 24.665462 -23.330925 0.125556 * *
XEC.4 192 15 23.051273 16.214163 -6.428326 0.000027 *
XEC.5 126 15 22.432474 16.154980 -6.309960 0.000025 *
MC.24 831 15 22.393442 18.004705 -10.009410 0.000161 *
KP.3.1 1957 15 21.637916 18.510306 -11.020613 0.000267 *
XEC.25 13 15 20.947831 13.497616 -0.995232 0.000002
XEC.32 42 15 19.732255 13.454761 -0.909521 0.000002
KP.3.1.1 12013 15 19.340654 16.323422 -6.646844 0.000030 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 273.484845 NaN NaN NaN * * *
KP.3.3 1715 4 251.001493 234.163823 -182.327646 1.282455e-15
XEC.9 305 17 242.162397 219.689373 -153.378745 6.631772e-22 *
XEC.2.2 273 24 240.646500 218.886472 -151.772944 2.964985e-22
XEC.18 165 4 238.577416 217.144635 -148.289270 5.204154e-23
XEC.39 155 4 237.246168 215.829008 -145.658015 1.397182e-23
XEC.38 34 4 237.102221 215.723331 -145.446663 1.257917e-23
XEC.6 45 1 235.300594 208.558100 -131.116200 9.725949e-27
XEC.4 192 4 234.974530 213.563471 -141.126942 1.450694e-24
XEC.14 193 6 234.785285 214.443992 -142.887983 3.497478e-24



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ259254


Target: 5350 samples Number of changes: 145
BC: XEC.6 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-10,16-145Gap history (edge excluded): 10-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.85e-33 Rec. model vs L2: 6.85e-25
Flags: Model_2BP_Bad_L1_opp

XEC.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.6 45 10 21.025611 NaN NaN NaN * * *
PG.3 31 10 20.727304 19.281664 -12.563327 0.759572 * *
XEC.28 39 10 18.857113 17.342480 -8.684961 0.109154 * *
XEC.4 192 14 15.813411 8.976300 8.047400 0.000025 *
MC.24 831 14 15.151503 10.762766 4.474469 0.000152 *
XEC.5 126 14 15.141493 8.863999 8.272003 0.000023 *
KP.3.1 1957 14 14.414457 11.286848 3.426305 0.000256 *
XEC.25 13 14 13.624849 6.174634 13.650732 0.000002
XFB.3 56 6 13.391693 6.606966 12.786068 0.000002
KP.2.28.1 10 6 13.318834 6.459999 13.080002 0.000002
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 280.689930 NaN NaN NaN * * *
KP.3.3 1715 4 250.866270 241.292405 -192.584810 1.183855e-15
XEC.9 305 16 249.326363 226.853339 -163.706678 6.371737e-22 *
XEC.2.2 273 23 247.671992 225.911965 -161.823929 2.476564e-22
XEC.18 165 16 240.865537 224.475328 -158.950656 5.897079e-23 *
XEC.39 155 16 239.508558 223.111877 -156.223753 1.506000e-23 *
XEC.38 34 16 239.225503 222.835294 -155.670589 1.143916e-23 *
XEC.15 127 26 239.170347 210.259030 -130.518061 3.954949e-29
XEC.14 193 16 238.057023 221.666814 -153.333628 3.550336e-24 *
XEC.29 135 26 235.472903 198.653095 -107.306190 3.607060e-34



Target sequence

, 21_C|T, 44_C|T, 222_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6027_C|T, 6183_A|G, 6476_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9679_C|T, 10029_C|T, 10198_C|T, 10369_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16323_C|T, 16362_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28651_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): OZ260197


Target: 5350 samples Number of changes: 140
BC: XEC.39 + XEK.5 BC BR: 48-49 BC BR coord: 21642 - 21643
Direction L1: << Initial region span: 1-45,49-140Gap history (edge excluded): 45-49
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.39e-16 Rec. model vs L2: 5.16e-60
Flags: Model_2BP_Bad_L1_opp

XEC.39 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.39 155 45 38.388351 NaN NaN NaN * * *
JN.1 17255 35 35.082955 8.702492 96.595016 2.368471e+03 *
LB.1.3 778 35 30.639802 -46.981661 207.963323 1.559378e-21
JN.1.13.1 751 35 30.478946 -27.966205 169.932410 2.825276e-13
LB.1 1128 35 27.504427 -24.832603 163.665205 6.462532e-12
KP.3.3 1715 35 26.542676 -9.338321 132.676642 3.465738e-05 *
XEC.16 23 45 26.473286 -22.433528 158.867056 7.123762e-11 *
XEC.17 13 45 26.473286 -22.573290 159.146580 6.193102e-11 *
XEC.24 11 45 26.473286 -22.573290 159.146580 6.193102e-11 *
XEC.32 42 45 26.449188 -9.721779 133.443557 2.370084e-05 * *
|||||

XEK.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.5 28 49 167.609174 NaN NaN NaN * * *
XEC.2 921 15 165.473003 153.682053 -113.364106 8.918214e-07
KP.3.3 1715 48 162.348195 159.657421 -125.314843 3.509033e-04 * *
XEC.36 30 49 159.756236 159.756236 -125.512473 3.878081e-04 * *
XEK.2 67 49 159.320949 159.320949 -124.641899 2.510145e-04 * *
KP.3.1.1 12013 49 158.943749 154.275478 -114.550956 1.616900e-06 *
XEC.19 59 48 157.436406 153.609593 -113.219187 8.315287e-07 *
XEC.15 127 48 157.035680 153.975517 -113.951035 1.197829e-06 *
XEC.2.2 273 48 156.139292 153.844414 -113.688828 1.051808e-06 *
XEC.31 66 48 155.698571 153.775635 -113.551270 9.806992e-07 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1929_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3682_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10396_G|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16257_T|C,
17410_C|T, 18116_A|G, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20151_T|C, 20400_A|G, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22264_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
26966_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28913_G|A, 28958_C|A,
29510_A|C, 29734_29759

Case 72 (XEC): USA/2607442/2025


Target: 5350 samples Number of changes: 143
BC: BA.5.11 + XEC.18 BC BR: 5-6 BC BR coord: 686 - 687
Direction L1: << Initial region span: 1-4,9-143Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 5.03e-08
Flags: Model_2BP_Bad_L1_opp

BA.5.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.5.11 989 4 8.106025 NaN NaN NaN * * *
HN.8 13 4 6.801549 -3.198451 18.396902 0.000013 * *
DE.1 90 5 6.620049 6.620049 -1.240099 0.247833 * *
BG.5 669 4 6.256906 5.277064 1.445873 0.064570 * *
BA.4.6 19369 5 5.986448 5.986448 0.027103 0.131336 * *
CM.2 356 4 5.668259 5.655743 0.688515 0.094420 * *
BQ.1.12 2465 4 5.363047 4.647657 2.704685 0.034562 * *
BA.5 6418 5 4.399094 4.399094 3.201813 0.026917 * *
BA.5.2.2 625 4 4.194037 3.464549 5.070903 0.010567 * *
BA.2.72 344 4 4.129940 2.205802 7.588396 0.002997 * *
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 9 262.874907 NaN NaN NaN * * *
XEC.14 193 13 260.502314 241.476221 -168.952441 6.604527e-03 *
XEC.19 59 19 260.246855 237.394599 -160.789198 1.116658e-04 *
KP.3.3 1715 13 259.567101 246.364005 -178.728010 8.780954e-01 *
XEC.2 921 19 258.077153 227.506625 -141.013250 5.659105e-09
XEC.33 169 13 250.232992 231.197954 -148.395908 2.277539e-07
XEC.2.2.1 46 19 249.832308 201.401210 -88.802420 2.603097e-20
XEK.1.2 33 19 249.196523 179.530173 -45.060346 8.269324e-30
XEC.2.1 265 19 248.840825 208.650527 -103.301054 3.665433e-17
XEC.29 135 19 247.254376 217.222809 -120.445619 1.941782e-13



Target sequence

, 241_C|T, 388_G|A, 509_523, 670_T|G, 686_694, 884_C|T, 897_C|A, 1780_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3213_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6198_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23285_G|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27476_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/AL-CDC-LC1136375/2025


Target: 5350 samples Number of changes: 147
BC: ML.2 + XEC.8 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,17-147Gap history (edge excluded): 4-17
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.94e-89 Rec. model vs L2: 1.36e-07
Flags: Model_2BP_Bad_L1_opp

ML.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
ML.2 67 4 10.429993 NaN NaN NaN * * *
XEC.5 126 7 7.088026 -5.313181 18.626363 1.452223e-07
KP.1.1.3 979 4 6.752912 6.752912 -5.505824 2.534941e-02 * *
LB.1 1128 4 6.623602 6.623602 -5.247205 2.225920e-02 * *
KP.2.3 4440 4 5.262138 5.262138 -2.524276 5.684569e-03 * *
BQ.1.1.13 384 3 5.209197 -4.790803 17.581606 2.454924e-07 *
BN.1 1200 3 4.758002 -5.241998 18.483997 1.565328e-07 *
BA.5.2.25 225 3 4.643280 -5.356720 18.713440 1.395281e-07 *
BA.2.6 424 3 4.011740 -5.988260 19.976520 7.394088e-08 *
JN.1 17255 4 3.898572 3.898572 0.202856 1.459006e-03 * *
|||||

XEC.8 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 17 239.838590 NaN NaN NaN * * *
XEC.2 921 17 235.955115 192.152673 -72.305346 6.983891e-13 *
XEC.31 66 17 233.874147 206.296200 -100.592401 9.660985e-07 *
XEC.13 30 9 230.779072 218.142681 -124.285362 1.353353e-01 *
XEC.4 192 17 226.152775 206.470555 -100.941109 1.150861e-06 *
XEC.9 305 17 225.877310 200.107992 -88.215984 1.990261e-09 *
XEC.5 126 3 225.426010 220.743758 -129.487515 1.822119e+00 *
KP.3.3 1715 17 224.619573 196.008512 -80.017024 3.298395e-11 *
XEC.16 23 17 222.913957 203.274296 -94.548592 4.714679e-08 *
XEC.15 127 32 218.705506 196.333501 -80.667001 4.565080e-11



Target sequence

, 241_C|T, 548_A|G, 670_T|G, 897_C|A, 1221_C|T, 2060_G|A, 2790_C|T, 2883_G|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 6504_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11647_T|C, 11727_G|A, 12119_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21759_A|G, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 25947_G|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/AZ-CDC-LC1136724/2025


Target: 5350 samples Number of changes: 146
BC: XEC.2.1 + JN.1.4 + XEC.2.1BC BR: 10-11, 29-30 BC BR coord: 4330 - 4331, 11726 - 11727
Direction L1: << Initial region span: 1-10,14-29,30-146Gap history (edge excluded): 10-30 -> 10-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.79e-01
Rec. model vs L1: 1.51e-27 Rec. model vs L2: 1.02e-67
Flags: Model_2BP_Best

XEC.2.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2.1 265 10 5.110242 None None None * * *
|||||

JN.1.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.4 8971 14 21.326646 NaN NaN NaN * * *
KP.3.1.1 12013 16 18.403504 0.446263 45.107473 1.122064e-02 *
JN.1 17255 16 17.393277 12.515814 20.968372 1.958629e+03 *
NL.19 18 16 13.363880 -9.423386 64.846772 5.801379e-07
JN.1.59 77 16 11.203885 -11.583381 69.166762 6.690447e-08
JN.1.16.1 466 16 10.959804 -11.833912 69.667823 5.210526e-08
NW.1 111 16 10.806076 -14.194619 74.389238 4.919790e-09
MC.42 84 16 10.676479 -16.497598 78.995197 4.907923e-10
BA.5.2.58 299 28 8.808574 -81.665569 209.331138 2.455262e-38
MC.19 221 16 8.767825 -18.406252 82.812504 7.304101e-11
|||||

XEC.2.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2.1 265 30 239.456143 NaN NaN NaN * * *
XEC.21 38 30 234.529655 255.972354 -251.944707 8.976945e+04 * *
XEC.29 135 30 228.715062 250.162069 -240.324138 2.690777e+02 * *
XEC.13 30 30 225.221545 246.657011 -233.314021 8.084915e+00 * *
XEC.39 155 1 220.009808 233.192331 -206.384661 1.147890e-05 *
XEC.31 66 30 218.854723 240.278288 -220.556576 1.377362e-02 * *
XEK.1 88 30 218.726667 223.898205 -187.796410 1.059997e-09 *
XEC.25 13 30 218.450885 239.920252 -219.840505 9.609530e-03 * *
XEK.5 28 30 218.334071 223.442929 -186.885858 6.725128e-10 *
XEC.33 169 30 218.310880 239.708276 -219.416552 7.789333e-03 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5833_C|T, 6183_A|G, 7216_T|C, 7842_A|G, 8248_T|A, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10738_T|C, 11042_G|T, 11083_G|T, 11288_11296, 11479_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18123_T|C, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26497_T|G, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28697_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-CDC-2-8448546/2025


Target: 5350 samples Number of changes: 144
BC: KP.3.3 + MC.33.1 + KP.3.3BC BR: 5-6, 9-10 BC BR coord: 2792 - 2793, 3566 - 3567
Direction L1: << Initial region span: 1-5,6-9,13-144Gap history (edge excluded): 5-13 -> 9-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.31e-01
Rec. model vs L1: 2.31e-07 Rec. model vs L2: 1.23e-156
Flags: Model_2BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 5 7.484405 None None None * * *
|||||

MC.33.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.33.1 85 9 12.609551 NaN NaN NaN * * *
KP.2.3.4 70 9 12.110560 12.110560 -16.221119 6.065307e-01 * *
KP.1.1 593 10 11.022576 9.944861 -11.889723 6.959935e-02 * *
XFG.3 480 9 10.103287 10.103287 -12.206575 8.167560e-02 * *
KP.3.1 1957 9 9.826179 9.826179 -11.652359 6.172909e-02 * *
JN.1.4 8971 9 7.237165 7.237165 -6.474330 4.630919e-03 * *
B.1.177.19 495 7 6.529220 -13.470780 34.941560 4.716284e-12
BF.14 1581 7 5.445294 -14.554706 37.109413 1.593641e-12
BA.2.9.7 243 7 4.728411 -15.271589 38.543179 7.795964e-13
BA.2.10.1 1369 7 4.540081 -15.459919 38.919837 6.446944e-13
|||||

KP.3.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 13 252.932900 NaN NaN NaN * * *
XEC.29 135 17 247.716863 211.551605 -119.103211 1.145706e-12
XEC.9 305 17 246.285430 218.002066 -132.004131 7.248909e-10
XEC.39 155 17 240.996777 218.809964 -133.619929 1.629488e-09
XEC.33 169 17 240.624092 229.368474 -154.736948 6.283489e-05 *
XEC.2 921 15 239.898054 210.334928 -116.669856 3.399425e-13
XEC.31 66 17 236.188008 206.073532 -108.147065 4.800770e-15
XEC.28 39 17 235.722025 218.895366 -133.790733 1.774051e-09
XEC.19 59 17 235.468024 206.467151 -108.934303 7.090646e-15
XEC.14 193 17 235.329662 213.142601 -122.285203 5.646417e-12



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3013_G|A, 3037_C|T, 3431_G|T, 3565_T|C, 3737_C|T, 3809_C|A, 4084_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6659_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14655_T|C, 15156_T|C,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22343_G|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23929_C|T, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146638/2025


Target: 5350 samples Number of changes: 143
BC: XEC.38 + XEC.2 BC BR: 11-12 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-8,12-143Gap history (edge excluded): 8-12
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.81e-28 Rec. model vs L2: 4.46e-19
Flags: Model_2BP_Bad_L1_opp

XEC.38 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.38 34 8 13.172332 NaN NaN NaN * * *
XEC.18 165 8 12.757409 4.904267 14.191466 0.660340 * *
XEC.5 126 8 11.936888 4.067746 15.864509 0.286505 * *
XEC.15 127 8 11.878843 4.025701 15.948597 0.273898 * *
XEC.9 305 8 11.022016 3.165590 17.668819 0.115903 * *
KP.3.3 1715 8 5.863847 -1.991046 27.982092 0.000669 * *
XEC.4.6 10 8 5.589794 -2.263348 28.526696 0.000508 * *
KP.3.1.1 12013 11 4.534174 4.534174 14.931653 0.456120 *
MC.24 831 8 3.990510 -3.865041 31.730083 0.000103 * *
KP.3.1 1957 8 3.885854 -3.970870 31.941740 0.000092 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 12 238.277608 NaN NaN NaN * * *
XEC.9 305 14 235.176910 222.703885 -155.407771 1.721327e-07
XEC.30 135 4 231.287337 224.635859 -159.271719 1.185910e-06
XEC.14 193 13 230.573028 220.573028 -151.146056 2.045579e-08 *
XEC.29 135 14 229.463795 209.076686 -128.153373 2.072190e-13
XEC.18 165 13 223.116326 213.116326 -136.232651 1.177550e-11 *
XEK.2 67 14 220.045290 200.719999 -111.439997 4.874154e-17
XEC.31 66 13 219.797799 209.797799 -129.595599 4.278516e-13 *
XEC.28 39 13 219.331816 202.357276 -114.714552 2.500177e-16 *
XEC.19 59 13 219.077815 202.290051 -114.580102 2.342834e-16 *



Target sequence

, 241_C|T, 670_T|G, 1191_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4321_C|T, 4890_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18012_T|A,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24208_C|A, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25429_G|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28297_T|C, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29530_C|T

Case 72 (XEC): USA/CA-CDPH-500146752/2025


Target: 5350 samples Number of changes: 139
BC: XEC.14 + GW.5.2 + XEC.14BC BR: 5-6, 8-9 BC BR coord: 2792 - 2793, 3430 - 3431
Direction L1: << Initial region span: 1-5,7-8,9-139Gap history (edge excluded): 5-9 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.97e-04
Rec. model vs L1: 7.27e-09 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.14 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 4.213472 None None None * * *
|||||

GW.5.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
GW.5.2 13 7 8.004421 NaN NaN NaN * * *
NL.2 237 7 6.876263 -3.123737 12.247475 0.323033 * *
NL.19 18 7 6.069561 -3.930439 13.860878 0.144424 * *
BF.7.4.2 154 7 5.714739 -4.285261 14.570521 0.101266 * *
JN.1.1.2 17 7 5.433572 -4.566428 15.132856 0.076536 * *
B.1.293 36 7 5.376414 -4.623586 15.247173 0.072078 * *
JN.1.7.3 19 7 5.322346 -4.677654 15.355307 0.068221 * *
BN.1.2.6 25 7 5.047910 -4.952090 15.904181 0.052079 * *
B.1.439 85 7 4.922746 -5.077254 16.154507 0.045959 * *
HZ.3 65 7 4.785545 -5.214455 16.428909 0.039955 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 268.306840 NaN NaN NaN * * *
XEC.17 13 9 267.094491 279.176919 -266.353838 776.657923 * *
MC.24.1 25 9 264.690577 276.078257 -260.156514 35.163197 * *
XEC.32 42 9 263.851395 275.933823 -259.867646 30.416949 * *
XEC.4 192 9 263.429305 275.495985 -258.991969 19.589623 * *
XEC.13 30 9 263.168841 275.251269 -258.502539 15.332887 * *
XEC.38 34 9 263.150639 275.203214 -258.406429 14.658201 * *
XEC.18 165 9 262.930734 274.994925 -257.989849 11.881707 * *
XEC.24 11 9 262.864692 274.947120 -257.894240 11.302229 * *
XEC.40 52 9 262.844209 274.887801 -257.775602 10.697392 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 2950_T|C, 3037_C|T, 3157_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12937_A|G, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18483_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146814/2025


Target: 5350 samples Number of changes: 146
BC: XEC.8 + ML.1 BC BR: 138-139 BC BR coord: 28361 - 28362
Direction L1: >> Initial region span: 1-138,140-146Gap history (edge excluded): 138-140
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.03e-08 Rec. model vs L2: 8.68e-105
Flags: Model_2BP_Bad_L1_opp

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 138 238.071288 NaN NaN NaN * * *
XEC.18 165 138 229.630397 229.630397 -159.260795 2.160502e-04 * *
XEC.2 921 138 207.791442 207.791442 -115.582884 7.072339e-14 *
XEC.39 155 138 207.345136 207.345136 -114.690272 4.532127e-14 *
KP.3.3 1715 146 206.689729 192.967116 -85.934231 2.577196e-20
XEC.40 52 138 202.553265 202.553265 -105.106530 3.767311e-16 *
MC.24.1 25 138 198.183060 198.183060 -96.366120 4.766116e-18 *
XEC.5 126 138 195.644128 195.644128 -91.288256 3.758864e-19 *
XEC.9 305 138 194.894561 194.894561 -89.789121 1.775562e-19 *
XEC.30 135 138 194.239998 194.239998 -88.479996 9.223014e-20 *
|||||

ML.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
ML.1 13 140 13.599755 NaN NaN NaN * * *
KP.3.3 1715 139 12.580304 12.580304 -1.160607 7.942632e+03 * *
KP.3.3.4 292 140 10.380879 0.380879 23.238242 3.995506e-02 * *
MC.25 26 144 7.903615 -18.702477 61.404955 2.066489e-10
MC.8.1 174 140 7.444087 -8.615746 41.231492 4.955562e-06 *
KP.4.1 198 140 7.294941 -2.705059 29.410119 1.827146e-03 * *
LF.7.9.1 48 144 7.068786 -11.276717 46.553434 3.466327e-07
KR.1 62 144 6.968144 -18.073991 60.147982 3.860709e-10
MC.13.2 74 144 6.777607 -11.567896 47.135792 2.580790e-07
MC.21 25 144 6.597363 -11.748140 47.496280 2.155657e-07



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3896_G|A, 4184_G|A, 4321_C|T, 6183_A|G, 6226_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 8869_T|C, 9344_C|T, 9424_A|G,
9534_C|T, 9565_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18105_G|T, 18163_A|G, 18294_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21766_A|T, 21767_21772, 21941_G|T, 21987_G|A, 21992_21994, 22000_C|T, 22009_C|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28618_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29171_C|T, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146886/2025


Target: 5350 samples Number of changes: 144
BC: XEC.8 + LC.1 + XEC.8 BC BR: 8-9, 11-12 BC BR coord: 3566 - 3567, 4330 - 4331
Direction L1: << Initial region span: 1-8,9-11,14-144Gap history (edge excluded): 8-14 -> 11-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.41e-01
Rec. model vs L1: 1.86e-08Rec. model vs L2: 7.77e-122
Flags: Model_2BP_Best

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 8 19.202242 None None None * * *
|||||

LC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LC.1 10 11 10.630590 NaN NaN NaN * * *
BA.5.1.36 33 11 9.947494 9.947494 -11.894987 0.504090 * *
NY.7 36 11 9.637339 9.637339 -11.274677 0.369723 * *
JN.1.1.3 30 11 9.126513 9.126513 -10.253026 0.222017 * *
KP.4.1 198 11 8.332992 8.332992 -8.665985 0.100761 * *
KL.1 39 11 8.171002 8.171002 -8.342003 0.085435 * *
XBB.1.5.25 43 11 7.838524 7.838524 -7.677047 0.061421 * *
XBB.2.3.2 378 10 7.121335 1.952073 4.095854 0.000170 * *
XBB.1.16.14 142 11 6.878736 6.878736 -5.757472 0.023518 * *
BE.1.3 218 11 6.440873 6.440873 -4.881746 0.015146 * *
|||||

XEC.8 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 14 230.814875 NaN NaN NaN * * *
XEC.2 921 14 224.156876 208.875386 -115.750773 6.591961e-10 *
XEC.2.2 273 14 218.046162 193.118221 -84.236442 9.477747e-17 *
KP.3.3 1715 15 211.959277 205.883036 -109.766072 3.314928e-11 *
XEC.32 42 14 211.675701 210.998210 -119.996420 5.519382e-09 *
XEC.4 192 14 209.961763 209.225965 -116.451929 9.354438e-10 *
XEC.31 66 14 202.380560 201.657267 -101.314535 4.824013e-13 *
XEC.28 39 14 201.989329 194.232704 -86.465408 2.890303e-16 *
XEC.14 193 14 201.687488 200.968193 -99.936386 2.431738e-13 *
XEC.19 59 14 201.664230 194.146789 -86.293579 2.641538e-16 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3949_T|C, 4184_G|A, 4321_C|T, 5365_C|T, 5800_G|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10460_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18739_G|A, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22116_A|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23608_G|T, 23854_C|A, 23948_G|T, 24376_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26822_C|T, 26833_C|T, 26858_C|T, 27134_T|C, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146959/2025


Target: 5350 samples Number of changes: 139
BC: XEC.4.3 + XEC.28 BC BR: 12-13 BC BR coord: 5304 - 5305
Direction L1: << Initial region span: 1-5,13-139Gap history (edge excluded): 5-13
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.81e-42 Rec. model vs L2: 3.85e-17
Flags: Model_2BP_Bad_L1_opp

XEC.4.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.3 10 5 10.690412 NaN NaN NaN * * *
XEC.12 71 5 7.632120 -3.009515 54.019029 4.573003e-02 * *
XEC.18 165 5 7.475508 -3.155902 54.311804 3.955750e-02 * *
KP.3.1.1 12013 12 5.510809 5.510809 36.978383 2.292928e+02 *
GJ.1.1 34 3 4.903037 -48.153258 144.306517 1.132341e-21
BA.2.9.5 117 3 4.738576 -52.375476 152.750953 1.664387e-23
BN.1.2.4 31 3 4.724144 -62.625128 173.250255 5.884858e-28
BA.5.5 23560 5 4.497932 -11.484322 70.968644 9.540163e-06 *
XEC.29 135 9 4.381687 -3.478890 54.957779 2.858137e-02 *
BQ.1.1.61 45 3 4.328996 -49.500977 147.001953 2.950197e-22
|||||

XEC.28 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.28 39 13 271.616993 NaN NaN NaN * * *
XEC.2 921 7 271.327088 268.742601 -271.485203 5.669893e-02 *
XEC.14 193 4 267.240268 258.939453 -251.878906 3.128365e-06
XEC.39 155 7 264.205192 252.702429 -239.404858 6.099860e-09
XEC.31 66 11 261.944657 259.797799 -253.595599 7.392830e-06
XEC.9 305 4 260.403643 253.284773 -240.569546 1.094919e-08
XEC.17 13 11 259.858296 257.711438 -249.422875 9.143979e-07
XEC.19 59 13 259.077815 259.077815 -252.155630 3.598476e-06 *
MC.24.1 25 11 257.454382 255.307524 -244.615049 8.295231e-08
XEC.15 127 11 256.939211 254.792353 -243.584705 4.931685e-08



Target sequence

, 241_C|T, 670_T|G, 1150_C|T, 2060_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3768_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14346_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146960/2025


Target: 5350 samples Number of changes: 139
BC: XEC.4.3 + XEC.14 BC BR: 4-5 BC BR coord: 1153 - 1154
Direction L1: << Initial region span: 1-4,5-139Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.08e-27 Rec. model vs L2: 3.85e-17
Flags: Model_2BP_Bad_L1_opp

XEC.4.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.3 10 4 10.581513 NaN NaN NaN * * *
KP.3.3.10 55 4 9.569912 9.569912 -11.139824 0.364219 * *
JN.1.34 83 4 8.927300 8.927300 -9.854600 0.191092 * *
KS.2 18 4 8.837955 8.837955 -9.675911 0.175520 * *
MC.10 221 4 8.648716 8.648716 -9.297431 0.145148 * *
KP.2.3.13 25 4 8.566610 8.566610 -9.133220 0.133320 * *
JN.1.40 26 4 8.488168 8.488168 -8.976337 0.123687 * *
LZ.1 28 4 8.453281 8.453281 -8.906562 0.119433 * *
NY.7 36 4 8.201967 8.201967 -8.403933 0.092551 * *
JN.1.48.1 53 4 7.776727 7.776727 -7.553455 0.060507 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 277.240268 NaN NaN NaN * * *
XEC.28 39 8 274.029392 271.367026 -250.734052 2.808794e-03 *
XEC.9 305 5 270.403643 270.403643 -248.807286 1.075467e-03 * *
XEC.2 921 8 270.267362 251.343484 -210.686967 5.674719e-12
XEC.18 165 1 267.652679 260.292150 -228.584300 4.352197e-08
XEC.17 13 8 267.098377 264.461986 -236.923971 2.816544e-06
MC.24.1 25 8 264.694464 261.404146 -230.808292 1.327232e-07
XEC.29 135 5 264.350938 264.350938 -236.701875 2.523156e-06 *
XEC.15 127 8 264.097279 261.460888 -230.921775 1.402275e-07
XEC.32 42 8 263.855281 261.218890 -230.437780 1.103068e-07



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 2060_G|A, 2790_C|T, 2902_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14346_G|A, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146970/2025


Target: 5350 samples Number of changes: 143
BC: XEC.4 + MC.11 BC BR: 140-141 BC BR coord: 28883 - 28884
Direction L1: >> Initial region span: 1-135,141-143Gap history (edge excluded): 135-141
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.26e-06 Rec. model vs L2: 8.78e-121
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 135 272.368594 NaN NaN NaN * * *
XEC.9 305 135 245.645723 241.867956 -183.735912 2.549816e-12 *
XEC.39 155 135 245.430082 241.639328 -183.278655 2.025914e-12 *
XEC.12 71 135 244.154187 240.376420 -180.752840 5.717926e-13 *
KP.3.3 1715 141 240.977300 237.369000 -174.737999 2.832589e-14
MC.24.1 25 135 240.527506 236.095813 -172.191626 7.915132e-15 *
XEC.32 42 135 236.999882 233.222115 -166.444230 4.465412e-16 *
XEC.8 592 135 232.153215 228.375448 -156.750895 3.513215e-18 *
XEC.24 11 135 231.567155 221.586271 -143.172541 3.952258e-21 *
XEC.18 165 135 231.024563 221.565082 -143.130165 3.873998e-21 *
|||||

MC.11 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.11 393 141 6.592898 NaN NaN NaN * * *
KP.3.1 1957 137 5.468303 5.040140 -2.080280 0.211189 *
KP.3.1.1 12013 141 3.166689 3.166689 1.666621 0.032387 * *
JN.1 17255 141 2.880376 2.880376 2.239248 0.024355 * *
KP.3.3.1 211 136 0.527997 -6.481903 20.963806 0.000002



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2054_G|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6322_T|C, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20157_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25039_T|C, 25207_C|T, 25521_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28531_C|T, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29468_G|C, 29510_A|C

Case 72 (XEC): USA/CA-CDPH-500146971/2025


Target: 5350 samples Number of changes: 143
BC: XEC.32 + XBB.1.5.32 + XEC.32BC BR: 3-4, 6-7 BC BR coord: 896 - 897, 1539 - 1540
Direction L1: << Initial region span: 1-3,4-6,7-143Gap history (edge excluded): 3-7 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.70e-07
Rec. model vs L1: 1.29e-20 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 3 4.718819 None None None * * *
|||||

XBB.1.5.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.1.5.32 734 6 10.203883 NaN NaN NaN * * *
GC.2 35 4 7.204670 -12.795330 31.590660 1.026188e-10
BA.2.9.1 448 4 7.204670 -12.795330 31.590660 1.026188e-10
GC.1 14 4 7.204670 -12.795330 31.590660 1.026188e-10
XBB.1.5.21 611 4 7.204670 -12.795330 31.590660 1.026188e-10
XBB.2.3 695 6 5.855443 5.855443 -5.710885 1.290681e-02 * *
XBB.1.5.76 79 5 5.807614 -4.192386 14.384772 5.601843e-07 *
BQ.1.1.68 694 6 5.572080 5.572080 -5.144161 9.706107e-03 * *
LY.1 178 5 5.281555 -4.718445 15.436890 3.297273e-07 *
BA.5.2.54 62 4 5.023446 -14.976554 35.953108 1.160019e-11
|||||

XEC.32 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 7 256.092276 NaN NaN NaN * * *
XEC.15 127 7 253.778424 258.481370 -214.962740 9.729575e-02 * *
XEC.2 921 8 252.085212 246.766770 -191.533540 7.949394e-07 *
XEC.28 39 7 251.832118 256.472318 -210.944637 1.303653e-02 * *
XEC.9 305 7 251.375146 256.057623 -210.115245 8.651695e-03 * *
XEC.8 592 7 249.630700 254.280707 -206.561414 1.459006e-03 * *
XEC.14 193 7 245.674335 250.367016 -198.734033 2.909338e-05 * *
XEC.17 13 7 244.461986 249.180805 -196.361610 8.895189e-06 *
XEC.29 135 7 243.813481 248.532300 -195.064600 4.643696e-06 *
MC.24.1 25 7 241.404146 246.082143 -190.164287 4.007212e-07 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1230_A|G, 1302_C|T, 1537_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14403_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19255_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23464_T|C,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28498_C|T,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29708_C|T

Case 72 (XEC): USA/CA-CDPH-500146973/2025


Target: 5350 samples Number of changes: 140
BC: XBB.2.3.11 + XEC.32 BC BR: 4-5 BC BR coord: 1539 - 1540
Direction L1: << Initial region span: 1-4,5-140Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.40e-14
Flags: Model_2BP_Bad_L1_opp

XBB.2.3.11 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBB.2.3.11 240 4 6.996488 NaN NaN NaN * * *
DY.1 151 3 6.634900 -3.365100 16.730200 0.000032 * *
BQ.1.1.68 694 4 5.994129 5.994129 -1.988257 0.367879 * *
BA.2.9.4 37 3 5.920999 -4.079001 18.158003 0.000015 * *
BF.7.4.2 154 3 5.181596 -4.818404 19.636807 0.000007 *
EY.1 81 3 4.707001 -5.292999 20.585998 0.000005 *
BA.5.2.18 582 3 4.359080 -5.640920 21.281840 0.000003 *
BA.2.3.13 70 3 4.184809 -5.815191 21.630382 0.000003 *
XBB.1.5.32 734 4 4.143742 4.143742 1.712516 0.057844 * *
CH.1.1.15 87 3 3.967396 -6.032604 22.065208 0.000002 *
|||||

XEC.32 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 5 266.092276 NaN NaN NaN * * *
XEC.15 127 5 263.778424 263.778424 -233.556848 9.926125e-02 * *
XEC.2 921 6 262.085212 252.085212 -210.170424 8.273815e-07 *
XEC.28 39 5 261.832118 261.832118 -229.664237 1.412230e-02 * *
XEC.9 305 5 261.375146 261.375146 -228.750292 8.959866e-03 * *
XEC.8 592 5 259.630700 259.630700 -225.261399 1.564796e-03 * *
XEC.14 193 5 255.674335 255.674335 -217.348670 2.997940e-05 * *
XEC.17 13 5 254.461986 254.461986 -214.923971 8.895189e-06 *
XEC.29 135 5 253.813481 253.813481 -213.626962 4.666972e-06 *
MC.24.1 25 5 251.404146 251.404146 -208.808292 4.191655e-07 *



Target sequence

, 241_C|T, 670_T|G, 1302_C|T, 1537_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T,
18894_C|T, 19255_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23464_T|C, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28498_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29708_C|T

Case 72 (XEC): USA/CA-CDPH-500147141/2025


Target: 5350 samples Number of changes: 145
BC: BF.7.14.4 + XEC.2 BC BR: 3-4 BC BR coord: 1086 - 1087
Direction L1: << Initial region span: 1-3,15-145Gap history (edge excluded): 3-15
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 1.15e-17
Flags: Model_2BP_Bad_L1_opp

BF.7.14.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BF.7.14.4 36 3 8.723240 NaN NaN NaN * * *
BF.7.14.1 39 3 8.723240 8.723240 -9.446479 1.000000 * *
BF.7.14 256 3 8.699648 8.699648 -9.399296 0.975310 * *
BF.7.14.5 65 3 8.691987 8.691987 -9.383974 0.965605 * *
BF.7.14.6 77 3 7.688789 7.688789 -7.377579 0.355226 * *
BQ.1.1.1 1179 4 6.377713 4.041056 -0.082112 0.009233 * *
BF.7.26 89 4 6.148014 4.223304 -0.446607 0.011109 * *
BA.2.75.1 232 3 5.906902 5.906902 -3.813803 0.059606 * *
BA.5.2.49 19 3 5.778801 5.778801 -3.557601 0.052602 * *
BQ.1.32 36 3 5.139721 5.139721 -2.279441 0.027737 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 256.201769 NaN NaN NaN * * *
XEC.18 165 8 240.910533 217.190855 -112.381709 6.175010e-06
XEC.19 59 29 225.880841 184.868632 -47.737264 5.678584e-20
XEK.1.2 33 29 225.131652 130.854745 60.290511 1.976167e-43
XEC.33 169 29 224.551586 194.553372 -67.106744 9.128136e-16
XEC.2.1 265 29 224.339400 165.353465 -8.706929 1.901005e-28
XEC.14 193 29 223.332651 189.092540 -56.185081 3.882703e-18
KP.3.3 1715 8 223.213774 214.490035 -106.980070 4.149947e-07
XEC.2.2.1 46 29 222.329755 148.013289 25.973423 5.601662e-36
XEC.29 135 26 216.040490 175.948870 -29.897740 7.591599e-24



Target sequence

, 241_C|T, 670_T|G, 1085_G|T, 1387_C|T, 1471_C|T, 2060_G|A, 2395_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4754_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10199_A|T, 10447_G|A, 10449_C|A, 10702_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25668_A|G, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27476_C|T, 27604_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29499_A|T, 29510_A|C

Case 72 (XEC): USA/CA-LACPHL-AY11141/2025


Target: 5350 samples Number of changes: 147
BC: XEC.2 + XEC.4.1 + XEC.2BC BR: 4-5, 7-8 BC BR coord: 941 - 942, 2789 - 2790
Direction L1: << Initial region span: 1-3,6-7,8-147Gap history (edge excluded): 3-8 -> 3-6
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.23e-07
Rec. model vs L1: 7.86e-16 Rec. model vs L2: 6.82e-52
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 3 4.681558 None None None * * *
|||||

XEC.4.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1 68 6 11.014494 NaN NaN NaN * * *
XEC.11 16 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.25 13 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.4.3 10 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.4.1.4 23 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.4 192 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.38 34 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.36 30 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.35.1 28 7 6.286401 -13.713599 33.427198 4.007212e-07 *
XEC.34 22 7 6.286401 -13.713599 33.427198 4.007212e-07 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 8 239.111912 NaN NaN NaN * * *
XEC.14 193 7 227.764683 226.984367 -149.968735 1.059816e-07 *
XEC.39 155 7 224.435789 223.894404 -143.788808 4.822372e-09 *
XEC.36 30 7 223.999669 212.432088 -120.864175 5.059114e-14 *
XEC.4 192 7 222.819634 211.236304 -118.472607 1.531414e-14 *
XEC.33 169 7 221.575180 209.983645 -115.967290 4.387574e-15 *
XEC.8 592 7 218.363432 206.738933 -109.477866 1.709774e-16 *
XEC.17 13 7 217.101708 205.534126 -107.068251 5.124057e-17 *
XEC.32 42 7 213.858612 202.291030 -100.582060 1.996772e-18 *
MC.24.1 25 7 213.494994 202.540517 -101.081034 2.563905e-18 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1711_T|C, 1714_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11137_T|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13665_C|T, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19524_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21411_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24382_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25453_A|C, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28775_C|A, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29785_T|C

Case 72 (XEC): USA/CA-LACPHL-AY11147/2025


Target: 5350 samples Number of changes: 145
BC: XEC.33 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,16-145Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01
Rec. model vs L1: 5.46e-32Rec. model vs L2: 3.98e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 14 17.783166 NaN NaN NaN * * *
XEC.4 192 14 17.681102 17.681102 -3.362204 9.003245e-01 * *
XEC.16 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.4.3 10 12 15.079158 -7.384864 46.769728 1.171677e-11
XEC.32 42 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.17 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.22 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.18.3 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.24 11 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.25 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 271.351893 NaN NaN NaN * * *
XEC.14 193 28 245.024085 230.424664 -184.849328 3.710592e-14
XEC.29 135 16 242.299684 232.299684 -188.599368 2.419610e-13 *
XEC.25 13 28 237.617708 216.556357 -157.112714 3.513813e-20
XEC.30 135 28 234.867262 220.260406 -164.520813 1.428367e-18
XEC.2.1 265 28 229.985151 205.687253 -135.374506 6.683403e-25
XEC.5 126 28 227.124600 212.525180 -149.050360 6.245568e-22
XEC.18 165 28 226.505286 211.905866 -147.811731 3.359768e-22
XEC.9 305 24 225.734380 215.706172 -155.412344 1.501856e-20
XEC.39 155 5 223.777073 209.859526 -143.719052 4.346875e-23



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T,
26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11224/2025


Target: 5350 samples Number of changes: 147
BC: XEC.22 + KP.3.3 BC BR: 14-15 BC BR coord: 7118 - 7119
Direction L1: << Initial region span: 1-12,15-147Gap history (edge excluded): 12-15
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.20e-03
Rec. model vs L1: 6.95e-48Rec. model vs L2: 2.62e-18
Flags: Model_1BP_Best

XEC.22 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.22 23 12 17.007649 NaN NaN NaN * * *
XEC.24 11 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.8.1 12 11 11.469367 -5.007853 42.015706 1.637377e-07 *
XEC.32 42 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.16 23 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.17 13 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.25 13 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.4.3 10 11 11.469367 -11.575692 55.151383 2.306776e-10 *
XEC.18.3 13 11 11.469367 -4.920842 41.841683 1.791576e-07 *
XEC.4.1.4 23 11 11.469367 -16.646216 65.292432 1.449214e-12 *
|||||

KP.3.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 15 228.780238 NaN NaN NaN * * *
XEC.2 921 14 224.859125 221.262449 -166.524898 5.421326e-04 * *
XEC.18 165 14 218.824983 215.215192 -154.430383 1.284681e-06 *
XEC.8 592 14 204.873712 201.263921 -126.527842 1.123020e-12 *
XEK.1 88 15 203.910097 203.910097 -131.820193 1.581598e-11 *
XEC.2.2 273 14 203.658322 200.048531 -124.097062 3.332112e-13 *
XEC.31 66 14 202.279959 198.670168 -121.340337 8.382878e-14 *
XEC.28 39 14 201.637429 198.027638 -120.055277 4.420228e-14 *
XEC.19 59 14 201.386508 197.776717 -119.553434 3.425308e-14 *
XEC.14 193 14 201.348784 197.738993 -119.477985 3.307496e-14 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1715_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4810_C|T, 5012_G|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11398_T|C, 11727_G|A, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22498_C|T, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24912_C|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25542_T|C, 25584_C|T, 25606_G|A,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27532_C|T, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29422_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11296/2025


Target: 5350 samples Number of changes: 140
BC: XEC.4 + BF.5.2 BC BR: 137-138 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-137,138-140Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.25e-09 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Bad_L1_opp

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 137 288.911961 NaN NaN NaN * * *
XEC.18 165 137 284.454555 284.454555 -276.909110 1.162032e-02 * *
XEC.8 592 140 277.301170 272.920885 -253.841771 1.136662e-07
MC.24.1 25 137 276.706342 276.706342 -261.412684 5.005366e-06 *
XEC.9 305 137 273.619054 273.619054 -255.238108 2.288956e-07 *
XEC.19 59 137 273.331153 273.331153 -254.662307 1.712742e-07 *
XEC.30 135 137 271.256368 271.256368 -250.512736 2.150458e-08 *
XEC.32 42 137 271.190311 271.190311 -250.380622 2.015124e-08 *
XEC.2 921 140 270.164997 265.683259 -239.366518 8.194277e-11
XEC.36 30 137 267.200870 267.200870 -242.401739 3.727922e-10 *
|||||

BF.5.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BF.5.2 12 138 8.862472 NaN NaN NaN * * *
BA.5.12 97 138 8.485647 8.485647 -10.971293 0.687289 * *
ER.1.1 61 138 6.859675 6.859675 -7.719350 0.135335 * *
XEK.1 88 138 6.359561 6.359561 -6.719122 0.082085 * *
BF.11.1 311 138 6.260167 6.260167 -6.520334 0.074274 * *
MC.10.2.1 11 138 6.233135 6.233135 -6.466269 0.072440 * *
CJ.1.2 100 138 6.226827 6.226827 -6.453655 0.071719 * *
ML.1 13 138 6.217480 6.217480 -6.434961 0.071005 * *
XDY.6 11 138 6.099603 6.099603 -6.199207 0.063292 * *
XBB.1.5.106 16 138 5.969256 5.969256 -5.938511 0.055576 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 2939_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5704_G|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21575_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29077_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11453/2025


Target: 5350 samples Number of changes: 146
BC: XEC.4 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-12,26-146Gap history (edge excluded): 12-26
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.33e-01
Rec. model vs L1: 4.25e-26Rec. model vs L2: 9.34e-25
Flags: Model_1BP_Best

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 12 24.875579 NaN NaN NaN * * *
XEC.25 13 6 17.475308 16.862247 -7.724494 3.304682e-04 *
KP.3.1.1 12013 24 16.601492 10.301168 5.397665 4.679053e-07
XEC.18 165 12 15.393039 15.393039 -4.786078 7.636394e-05 * *
MC.24.1 25 12 15.369184 15.369184 -4.738367 7.447850e-05 * *
XEC.19 59 12 14.459938 14.459938 -2.919875 2.997940e-05 * *
XEC.9 305 6 13.184990 12.525087 0.949825 4.329753e-06
XEC.8 592 6 13.170579 12.516266 0.967467 4.286672e-06
KP.3.1.12 39 4 11.473441 -7.416719 40.833437 9.476134e-15
JN.1 17255 16 10.826448 4.879750 16.240501 2.071485e-09
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 26 256.615521 NaN NaN NaN * * *
XEC.29 135 26 248.908513 201.011461 -112.022921 9.291656e-19 *
XEC.31 66 26 245.197181 211.304463 -132.608926 2.748874e-14 *
XEC.33 169 29 239.796743 201.045862 -112.091724 9.622622e-19
XEC.8 592 26 239.523761 215.185122 -140.370245 1.331121e-12 *
KP.3.3 1715 8 236.865542 227.512277 -165.024554 2.998450e-07
XEC.2.2 273 26 236.634910 195.099581 -100.199163 2.520071e-21 *
XEC.9 305 26 236.238169 196.262636 -102.525271 8.079152e-21 *
XEC.14 193 26 235.597621 201.704903 -113.409807 1.861777e-18 *
XEK.5 28 26 235.525893 182.299674 -74.599348 6.957342e-27 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 2939_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5784_C|T, 6183_A|G, 6361_C|T, 7842_A|G, 7865_G|T, 8293_C|T, 8393_G|A,
8950_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10093_T|A, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20483_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29670_C|T, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11538/2025


Target: 5350 samples Number of changes: 145
BC: XEC.2 + XEC.9 + XEC.2 BC BR: 4-5, 14-15 BC BR coord: 896 - 897, 6026 - 6027
Direction L1: << Initial region span: 1-4,6-14,15-145Gap history (edge excluded): 4-15 -> 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 2.71e-05
Rec. model vs L1: 1.20e-23Rec. model vs L2: 2.75e-33
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 4 3.75823 None None None * * *
|||||

XEC.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.9 305 6 18.888817 NaN NaN NaN * * *
KP.3.1.10 51 8 16.450958 -18.842803 59.685607 9.012443e-13
JN.1.7.1 120 8 15.377918 -14.622082 51.244164 6.162213e-11
KP.3.3 1715 8 14.119585 -4.150811 30.301622 2.171701e-06
JN.1.10 28 8 13.952536 -16.047464 54.094928 1.482064e-11
MC.10.1 650 7 13.877320 -6.122680 34.245360 3.013480e-07 *
MC.1 932 7 13.850540 -6.149460 34.298920 2.939077e-07 *
MU.2.1 37 8 13.759752 -16.240248 54.480495 1.219494e-11
KP.1.1 593 7 13.364870 -6.635130 35.270261 1.809582e-07 *
JN.1.32.1 55 8 13.335346 -16.664654 55.329309 7.972683e-12
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 287.015305 NaN NaN NaN * * *
KP.3.3 1715 8 274.513147 264.627067 -241.254135 4.397434e-12
XEC.4 192 6 259.202657 245.070275 -202.140550 1.414395e-20
XEC.39 155 16 257.129964 241.835838 -195.671675 5.567088e-22 *
XEC.32 42 8 256.167762 250.422434 -212.844868 2.978833e-18
XEC.9 305 6 255.461779 231.255438 -174.510876 1.415117e-26
XEC.29 135 17 252.990085 232.755617 -177.511235 6.342116e-26
XEK.1 88 17 243.910097 227.840467 -167.680934 4.652397e-28
XEC.2.2 273 16 243.658322 228.340171 -168.680343 7.670506e-28 *
XEC.31 66 16 242.279959 226.968244 -165.936488 1.949129e-28 *



Target sequence

, 241_C|T, 337_C|T, 670_T|G, 897_C|A, 1738_G|T, 2060_G|A, 2113_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5221_C|T, 6027_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23593_G|C, 23599_T|G, 23601_C|A, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25521_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY12004/2025


Target: 5350 samples Number of changes: 141
BC: KP.2.5 + XEC.14 BC BR: 3-4 BC BR coord: 678 - 679
Direction L1: << Initial region span: 1-3,5-141Gap history (edge excluded): 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.13e-145Rec. model vs L2: 1.66e-17
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.5 66 3 9.391444 NaN NaN NaN * * *
CM.3 22 3 6.639909 6.639909 -7.279818 0.063928 * *
BQ.1.1.7 1146 4 6.349948 2.677297 0.645407 0.001213 * *
KP.5 77 3 6.000082 6.000082 -6.000164 0.033709 * *
BN.1.2.3 117 3 5.653341 5.653341 -5.306682 0.023873 * *
BQ.1.26 121 3 5.611641 5.611641 -5.223282 0.022823 * *
BA.5.2.48 267 3 5.234796 5.234796 -4.469593 0.015686 * *
BF.7.24 444 3 4.319240 4.319240 -2.638479 0.006282 * *
BQ.1.11 1938 3 3.937737 3.937737 -1.875474 0.004296 * *
BF.3 355 3 3.844681 3.844681 -1.689363 0.003907 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 276.499648 NaN NaN NaN * * *
XEC.8 592 5 271.990858 261.990858 -225.981716 1.099846e-02 * *
XEC.9 305 5 269.837039 259.837039 -221.674078 1.274757e-03 * *
XEC.3 29 8 264.226759 254.140514 -210.281029 4.286672e-06
XEC.13 30 8 262.691703 252.605458 -207.210917 9.235878e-07
XEC.29 135 16 261.793841 241.762275 -185.524550 1.801169e-11
XEC.2 921 16 261.562400 231.368682 -164.737365 5.536494e-16
XEC.18 165 8 259.889050 249.790648 -201.581295 5.532727e-08
XEC.33 169 8 257.721668 247.605535 -197.211071 6.223085e-09
XEC.30 135 8 256.872574 246.748818 -195.497635 2.646574e-09



Target sequence

, 241_C|T, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY12040/2025


Target: 5350 samples Number of changes: 145
BC: XEC.4 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-12,26-145Gap history (edge excluded): 12-26
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.33e-01
Rec. model vs L1: 4.25e-26Rec. model vs L2: 9.34e-25
Flags: Model_1BP_Best

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 12 24.875579 NaN NaN NaN * * *
XEC.25 13 6 17.475308 16.862247 -7.724494 3.304682e-04 *
KP.3.1.1 12013 24 16.601492 10.301168 5.397665 4.679053e-07
XEC.18 165 12 15.393039 15.393039 -4.786078 7.636394e-05 * *
MC.24.1 25 12 15.369184 15.369184 -4.738367 7.447850e-05 * *
XEC.19 59 12 14.459938 14.459938 -2.919875 2.997940e-05 * *
XEC.9 305 6 13.184990 12.525087 0.949825 4.329753e-06
XEC.8 592 6 13.170579 12.516266 0.967467 4.286672e-06
KP.3.1.12 39 4 11.473441 -7.416719 40.833437 9.476134e-15
JN.1 17255 16 10.826448 4.879750 16.240501 2.071485e-09
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 26 266.615521 NaN NaN NaN * * *
XEC.29 135 26 258.908513 211.011461 -134.022921 9.291656e-19 *
XEC.31 66 26 255.197181 221.304463 -154.608926 2.748874e-14 *
XEC.33 169 29 249.796743 211.045862 -134.091724 9.622622e-19
XEC.8 592 26 249.523761 225.185122 -162.370245 1.331121e-12 *
KP.3.3 1715 8 246.865542 237.512277 -187.024554 2.998450e-07
XEC.2.2 273 26 246.634910 205.099581 -122.199163 2.520071e-21 *
XEC.9 305 26 246.238169 206.262636 -124.525271 8.079152e-21 *
XEC.14 193 26 245.597621 211.704903 -135.409807 1.861777e-18 *
XEK.5 28 26 245.525893 192.299674 -96.599348 6.957342e-27 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1102_C|T, 2060_G|A, 2790_C|T, 2939_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5784_C|T, 6183_A|G, 6361_C|T, 7842_A|G, 7865_G|T, 8293_C|T, 8393_G|A,
8950_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10093_T|A, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20483_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY12077/2025


Target: 5350 samples Number of changes: 147
BC: XEC.5 + XEC.2 BC BR: 13-14 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-10,15-147Gap history (edge excluded): 10-15
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.35e-01
Rec. model vs L1: 1.29e-28Rec. model vs L2: 4.90e-25
Flags: Model_1BP_Best

XEC.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.5 126 10 14.842864 NaN NaN NaN * * *
XEC.33 169 10 13.426664 5.573522 20.852955 2.465970e-01 * *
XEC.15 127 10 12.993314 5.140172 21.719657 1.596135e-01 * *
MC.1.2 49 4 11.386334 -8.149519 48.299037 2.699579e-07
MA.1.2 96 4 9.978552 -9.557301 51.114601 6.623876e-08
KP.1.1.1 578 4 8.185275 -11.396450 54.792900 1.051987e-08
LP.8.1.1 2345 4 6.779659 -19.354581 70.709161 3.673045e-12
JN.1 17255 4 4.792390 -4.820399 41.640799 7.542175e-06
MR.1 17 3 4.718819 -42.403648 116.807295 3.585407e-22
MC.17.1 10 3 4.718819 -24.922394 81.844788 1.406622e-14
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 235.334694 NaN NaN NaN * * *
XEC.9 305 16 235.222128 222.749103 -155.498207 7.539608e-02 * *
XEC.33 169 5 230.952196 220.067605 -150.135210 5.169393e-03 *
XEC.8 592 26 218.593270 205.772722 -121.545444 3.200368e-09
XEC.2.2 273 26 215.557666 195.099581 -100.199163 7.397864e-14
XEC.29 135 26 215.472903 188.653095 -87.306190 1.175110e-16
XEC.2.1 265 26 215.367090 192.845563 -95.691126 7.758402e-15
XEC.14 193 26 214.520377 201.704903 -113.409807 5.465393e-11
XEK.5 28 26 214.448649 182.299674 -74.599348 2.042382e-19
XEC.31 66 26 211.045951 198.230477 -106.460955 1.692186e-12



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 919_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3061_A|G, 3431_G|T, 3565_T|C, 3879_A|G, 4184_G|A, 4321_C|T, 5193_T|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9711_C|T, 10029_C|T, 10198_C|T, 10432_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15614_A|G,
15714_C|T, 15746_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24038_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25521_C|G,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28723_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/DC-CDC-2-8448731/2025


Target: 5350 samples Number of changes: 146
BC: XEC.33 + XEC.2 BC BR: 15-16 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-12,18-146Gap history (edge excluded): 12-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.76e-06
Rec. model vs L1: 5.15e-09Rec. model vs L2: 5.20e-19
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 12 13.225069 NaN NaN NaN * * *
XEC.17 13 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.25 13 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.24 11 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.8.1 12 11 11.469367 -15.007853 60.015706 0.000007 *
XEC.22 23 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.4.3 10 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.18.3 13 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.16 23 11 11.469367 -14.920842 59.841683 0.000008 *
XEC.32 42 11 11.469367 -14.920842 59.841683 0.000008 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 245.978085 NaN NaN NaN * * *
KP.3.3 1715 16 242.468094 238.091834 -190.183667 2.253727e-01 *
XEC.9 305 18 235.063472 222.583600 -159.167199 4.160689e-08 *
XEC.33 169 29 229.910330 221.143900 -156.287799 9.857828e-09
XEK.1.2 33 20 218.719356 198.546170 -111.092339 1.509128e-18
XEC.8 592 18 215.457227 209.058479 -132.116959 5.563299e-14 *
XEC.4.6.1 13 16 212.670454 206.015604 -126.031208 2.647925e-15
XEC.31 66 18 212.585065 206.188008 -126.376017 3.154331e-15 *
XEC.28 39 18 212.119082 205.722025 -125.444049 1.971464e-15 *
XEC.29 135 18 212.078102 197.117967 -108.235935 3.629579e-19 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1879_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4543_C|T, 5164_G|T, 6040_C|T, 6183_A|G, 7842_A|G, 7844_C|T, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11173_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16393_C|T, 17410_C|T, 18163_A|G, 18401_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25799_A|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27630_C|T, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29101_A|G, 29510_A|C

Case 72 (XEC): USA/DE-CDC-LC1136200/2025


Target: 5350 samples Number of changes: 143
BC: XEC.32 + LZ.5 BC BR: 140-141 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-140,141-143Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.36e-09 Rec. model vs L2: 1.63e-101
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 140 256.256839 NaN NaN NaN * * *
KP.3.3 1715 143 248.731067 245.653078 -191.306156 2.491601e-05 *
XEC.19 59 140 247.191129 247.191129 -194.382257 1.156433e-04 * *
XEC.39 155 140 246.656679 246.656679 -193.313357 6.772874e-05 * *
XEC.8 592 143 244.989738 241.025281 -182.050563 2.430497e-07
XEC.9 305 143 240.935604 234.766363 -169.532725 4.645277e-10
XEC.11 16 140 240.829204 240.829204 -181.658409 1.999897e-07 *
XEC.36 30 140 240.613602 240.613602 -181.227203 1.613000e-07 *
XEC.17 13 140 239.424370 239.424370 -178.848739 4.907088e-08 *
XEC.24 11 127 239.053640 235.194571 -170.389142 7.140986e-10
|||||

LZ.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LZ.5 14 141 8.697959 NaN NaN NaN * * *
BQ.1.33 11 141 7.293213 7.293213 -8.586427 0.245367 * *
XBB.1.4 50 141 7.104036 7.104036 -8.208073 0.202909 * *
HN.3 27 141 6.644733 6.644733 -7.289465 0.128093 * *
XEC.27 25 141 6.526721 6.526721 -7.053442 0.113608 * *
JN.1.7.7 13 141 6.448280 6.448280 -6.896559 0.105399 * *
XBB.1.5.89 23 141 6.348644 6.348644 -6.697287 0.095369 * *
BF.5.4 14 141 6.213052 6.213052 -6.426105 0.083326 * *
XEC.9 305 141 6.169241 6.169241 -6.338482 0.079659 * *
HN.7 28 141 6.066449 6.066449 -6.132898 0.071719 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4475_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10978_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22367_T|C, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25099_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27549_C|T, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29420_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/DE-USAFSAM-S23724/2025


Target: 5350 samples Number of changes: 141
BC: XEC.32 + LZ.5 BC BR: 138-139 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-138,139-141Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 8.32e-09 Rec. model vs L2: 9.36e-101
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 138 258.687290 NaN NaN NaN * * *
KP.3.3 1715 141 255.114028 252.036038 -206.072077 1.294022e-03 *
XEC.19 59 138 253.833234 253.833234 -209.666467 7.828378e-03 * *
XEC.8 592 141 251.478482 247.514026 -197.028051 1.409064e-05 *
XEC.39 155 138 249.274098 249.274098 -200.548196 8.190095e-05 * *
XEC.9 305 141 247.346353 241.177111 -184.354223 2.486014e-08
XEC.14 193 141 243.834503 239.020505 -180.041010 2.881370e-09
XEC.11 16 138 243.526719 243.526719 -189.053437 2.606728e-07 *
XEC.36 30 138 243.100395 243.100395 -188.200790 1.704200e-07 *
XEC.4 192 138 242.050643 242.050643 -186.101287 5.963638e-08 *
|||||

LZ.5 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LZ.5 14 139 8.697959 NaN NaN NaN * * *
BQ.1.33 11 139 7.293213 7.293213 -8.586427 0.245367 * *
XBB.1.4 50 139 7.104036 7.104036 -8.208073 0.202909 * *
HN.3 27 139 6.644733 6.644733 -7.289465 0.128093 * *
XEC.27 25 139 6.526721 6.526721 -7.053442 0.113608 * *
JN.1.7.7 13 139 6.448280 6.448280 -6.896559 0.105399 * *
XBB.1.5.89 23 139 6.348644 6.348644 -6.697287 0.095369 * *
BF.5.4 14 139 6.213052 6.213052 -6.426105 0.083326 * *
XEC.9 305 139 6.169241 6.169241 -6.338482 0.079659 * *
HN.7 28 139 6.066449 6.066449 -6.132898 0.071719 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4475_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 10978_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22367_T|C, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27549_C|T, 27807_C|T, 27810_T|C, 28093_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29420_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/FL-CDC-LC1136791/2025


Target: 5350 samples Number of changes: 146
BC: KP.3.1.1 + XEC.25 BC BR: 29-30 BC BR coord: 10520 - 10521
Direction L1: << Initial region span: 1-15,30-146Gap history (edge excluded): 15-30
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.96e-74 Rec. model vs L2: 2.08e-18
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 15 13.768491 NaN NaN NaN * * *
BF.11 2573 4 8.632640 -98.631561 281.263121 8.444995e-42
XEC.29 135 9 7.073173 -30.572888 145.145776 3.037458e-12
BF.11.2 418 3 6.710957 -154.574374 393.148748 4.265742e-66
BF.11.1 311 3 6.709306 -136.718397 357.436794 2.422828e-58
BF.11.5 122 3 6.707517 -164.682541 413.365082 1.734912e-70
BF.11.4 202 3 6.700834 -142.814352 369.628704 5.461321e-61
NY.16 136 5 6.305066 -56.928874 197.857749 1.088126e-23
KP.3.3.1 211 5 6.159968 -25.195072 134.390145 6.591961e-10
JN.1.9 576 5 5.965395 -34.571607 153.143213 5.591185e-14
|||||

XEC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.25 13 30 258.133541 NaN NaN NaN * * *
XEC.8 592 30 257.929424 257.929424 -275.858849 8.146473e-01 * *
XEC.9 305 30 255.586242 255.586242 -271.172484 7.808167e-02 * *
XEC.2 921 30 254.855862 254.855862 -269.711724 3.762826e-02 * *
XEC.40 52 30 250.218231 250.218231 -260.436463 3.652239e-04 * *
XEC.31 66 17 245.529196 243.254953 -246.509905 3.449039e-07
KP.3.3 1715 30 245.265231 245.265231 -250.530462 2.574127e-06 *
XEK.1 88 30 243.126897 243.126897 -246.253794 3.028585e-07 *
XEC.2.1 265 30 242.933619 242.933619 -245.867237 2.504516e-07 *
XEC.29 135 30 242.822062 242.822062 -245.644123 2.232441e-07 *



Target sequence

, 140_C|T, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3448_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 5826_C|T, 6183_A|G, 6607_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9556_T|C, 10029_C|T, 10198_C|T, 10416_C|T, 10447_G|A, 10449_C|A, 10519_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19497_T|C, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 21998_C|T, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IL-RIPHL_124021_G/2025


Target: 5350 samples Number of changes: 145
BC: KP.2.2 + XEC.2 BC BR: 5-6 BC BR coord: 1713 - 1714
Direction L1: << Initial region span: 1-5,7-145Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.09e-87 Rec. model vs L2: 1.05e-11
Flags: Model_2BP_Bad_L1_opp

KP.2.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.2 1334 5 9.029481 NaN NaN NaN * * *
KW.1.1 127 4 7.613024 -2.386976 16.773953 1.102881e-05 * *
MC.43 131 4 7.599120 -2.400880 16.801761 1.086461e-05 * *
CL.1 688 3 7.215446 -12.784554 37.569109 3.356339e-10
JN.1.1 3081 4 7.081387 -2.918613 17.837226 6.459233e-06 *
KP.3.3 1715 4 6.628465 -3.371535 18.743070 4.118589e-06 *
JN.1.19 438 4 6.390614 -10.400399 32.800797 3.644670e-09 *
MC.16 917 4 6.354086 -3.645914 19.291828 3.128365e-06 *
MC.1 932 4 6.314172 -3.685828 19.371655 3.005700e-06 *
KP.2.3 4440 4 6.021946 -3.978054 19.956108 2.237839e-06 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 249.082219 NaN NaN NaN * * *
XEC.39 155 6 234.435789 234.435789 -170.871578 9.609530e-03 * *
XEC.14 193 6 228.083666 228.083666 -158.167331 1.678542e-05 * *
XEC.17 13 6 227.101708 227.101708 -156.203415 6.268334e-06 *
XEC.15 127 6 224.274571 224.274571 -150.549141 3.717665e-07 *
XEC.32 42 6 223.858612 223.858612 -149.717224 2.454924e-07 *
MC.24.1 25 6 223.494994 223.494994 -148.989989 1.704200e-07 *
XEC.4 192 6 223.133422 223.133422 -148.266844 1.188980e-07 *
XEC.38 34 6 223.036607 223.036607 -148.073214 1.075833e-07 *
XEC.24 11 6 222.871909 222.871909 -147.743818 9.121924e-08 *



Target sequence

, 241_C|T, 443_G|A, 670_T|G, 897_C|A, 1711_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4927_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8412_A|G, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11137_T|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13665_C|T, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21411_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25453_A|C, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759, 29785_T|C

Case 72 (XEC): USA/IL-RIPHL_124096_G/2025


Target: 5350 samples Number of changes: 147
BC: KP.2.3.7 + XEC.14 BC BR: 6-7 BC BR coord: 1651 - 1652
Direction L1: << Initial region span: 1-6,11-147Gap history (edge excluded): 6-11
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.03e-01
Rec. model vs L1: 1.73e-154Rec. model vs L2: 5.05e-17
Flags: Model_1BP_Best

KP.2.3.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.7 54 6 16.853608 NaN NaN NaN * * *
XEC.11.1 166 9 14.746054 7.378559 -0.757117 7.674671e-05 *
JN.1.53 62 6 14.228038 14.228038 -14.456075 7.243976e-02 * *
KP.5 77 6 13.906467 13.906467 -13.812933 5.233971e-02 * *
KP.3.3.3 288 6 12.833681 12.833681 -11.667362 1.795296e-02 * *
LA.1 149 6 12.440820 12.440820 -10.881641 1.209455e-02 * *
LF.7.9.3 20 5 11.825673 1.825673 10.348653 2.968615e-07 *
XFB.3 56 5 11.670112 1.670112 10.659776 2.542367e-07 *
XEL.5 19 5 11.593891 1.593891 10.812218 2.358665e-07 *
LC.1 10 5 11.297148 1.297148 11.405704 1.747342e-07 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 11 234.385154 NaN NaN NaN * * *
KP.3.3 1715 11 229.858678 222.667042 -127.334083 1.127881e-04 * *
XEC.17 13 11 219.734212 217.101708 -116.203415 4.319310e-07 *
XEC.21 38 11 219.337069 208.969159 -99.938317 1.272331e-10 *
XEC.31 66 41 219.196756 211.092222 -104.184444 1.059997e-09
XEC.40 52 41 219.182933 205.054631 -92.109262 2.537099e-12
XEK.1 88 41 219.068700 167.385281 -16.770562 1.107807e-28
XEC.2.1 265 41 218.882998 184.871171 -51.742343 4.346135e-21
XEC.25 13 41 218.792918 212.084697 -106.169394 2.866999e-09
XEC.29 135 41 218.771300 204.570922 -91.141843 1.562084e-12



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1651_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3379_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12669_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12965_T|C, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17172_C|A, 17343_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25603_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29109_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IL-RIPHL_124110_G/2025


Target: 5350 samples Number of changes: 145
BC: KP.2.3.7 + XEC.14 BC BR: 4-5 BC BR coord: 1651 - 1652
Direction L1: << Initial region span: 1-4,9-145Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.73e-154Rec. model vs L2: 3.47e-17
Flags: Model_2BP_Bad_L1_opp

KP.2.3.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.7 54 4 13.173619 NaN NaN NaN * * *
XEC.11.1 166 7 11.010599 3.643104 2.713793 0.000073 *
JN.1.53 62 4 10.131202 10.131202 -10.262404 0.047596 * *
KP.5 77 4 9.783441 9.783441 -9.566882 0.033709 * *
LA.1 149 4 9.250311 9.250311 -8.500622 0.019742 * *
KP.3.3.3 288 4 8.580112 8.580112 -7.160223 0.010102 * *
JN.1.9 576 4 7.897534 7.897534 -5.795069 0.005118 * *
KP.2.3 4440 4 7.454984 7.454984 -4.909967 0.003280 * *
LP.8.1.1 2345 4 6.469249 6.469249 -2.938498 0.001225 * *
JN.1.1 3081 4 6.211840 6.211840 -2.423679 0.000944 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 234.385154 NaN NaN NaN * * *
KP.3.3 1715 9 229.858678 222.667042 -127.334083 1.127881e-04 * *
XEC.17 13 9 219.734212 217.101708 -116.203415 4.319310e-07 *
XEC.21 38 9 219.337069 208.969159 -99.938317 1.272331e-10 *
XEC.31 66 39 219.196756 211.092222 -104.184444 1.059997e-09
XEC.40 52 39 219.182933 205.054631 -92.109262 2.537099e-12
XEK.1 88 39 219.068700 167.385281 -16.770562 1.107807e-28
XEC.2.1 265 39 218.882998 184.871171 -51.742343 4.346135e-21
XEC.25 13 39 218.792918 212.084697 -106.169394 2.866999e-09
XEC.29 135 39 218.771300 204.570922 -91.141843 1.562084e-12



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1651_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3379_A|G, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12669_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12965_T|C, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17172_C|A, 17343_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25603_C|A, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29109_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IL-RIPHL_124115_G/2025


Target: 5350 samples Number of changes: 144
BC: JN.1.61 + XEC.2 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,7-144Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.80e-100Rec. model vs L2: 7.00e-08
Flags: Model_2BP_Bad_L1_opp

JN.1.61 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.61 13 4 12.830988 NaN NaN NaN * * *
JN.1.31 204 4 11.399343 11.399343 -12.798685 2.393089e-01 * *
MC.3 68 4 11.146800 11.146800 -12.293599 1.854444e-01 * *
BF.10.1 37 3 8.157665 -1.842335 13.684670 4.255004e-07 *
BA.5 6418 3 5.390395 -4.609605 19.219209 2.666271e-08 *
BA.4.6 19369 3 3.683843 -10.215003 30.430006 9.810331e-11 *
BA.5.1.22 4997 3 3.240544 -6.759456 23.518912 3.105783e-09 *
XEC.25 13 5 1.005220 -5.281181 20.562362 1.364354e-08 *
XEC.24 11 5 1.005220 -5.281181 20.562362 1.364354e-08 *
XEC.29 135 5 1.005220 -5.281181 20.562362 1.364354e-08 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 254.773388 NaN NaN NaN * * *
XEC.39 155 3 240.652038 235.950730 -171.901459 3.238143 *
XEC.25 13 3 240.255109 235.540855 -171.081710 2.148994 *
XEC.18 165 3 239.990716 235.288621 -170.577242 1.673639 *
XEC.33 169 3 237.817906 233.133541 -166.267082 0.193980 *
XEC.8 592 3 236.165715 231.520273 -163.040547 0.038581 *
XEC.17 13 3 231.815961 227.101708 -154.203415 0.000464 *
XEC.14 193 7 231.797265 228.083666 -156.167331 0.001243 * *
XEC.15 127 3 230.743005 226.044625 -152.089250 0.000162 *
XEC.31 66 15 228.670168 221.092222 -142.184444 0.000001



Target sequence

, 241_C|T, 347_G|T, 670_T|G, 897_C|A, 2060_G|A, 2069_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6543_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18075_T|C,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25669_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27795_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28352_A|G, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29358_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IL-USAFSAM-S23723/2025


Target: 5350 samples Number of changes: 142
BC: XEC.4 + JN.1.39 + XEC.4BC BR: 11-12, 16-17 BC BR coord: 4330 - 4331, 8292 - 8293
Direction L1: << Initial region span: 1-11,13-16,17-142Gap history (edge excluded): 11-17 -> 11-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.45e-06
Rec. model vs L1: 1.98e-12 Rec. model vs L2: 2.29e-86
Flags: Model_2BP_Best

XEC.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 11 11.411059 None None None * * *
|||||

JN.1.39 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.39 1007 13 9.471030 NaN NaN NaN * * *
JN.1.4 8971 13 8.094207 -1.905793 21.811586 2.528396e-01 * *
KS.1.1.2 252 15 8.088122 -14.898127 47.796254 5.743654e-07
MC.1 932 14 7.121538 -3.654406 25.308813 4.393693e-02 * *
MC.1.3 51 15 7.120776 -13.656244 45.312488 1.994734e-06
NL.12 51 15 7.120776 -9.269433 36.538866 1.600539e-04 *
JN.1.7.4 101 15 7.120678 -9.269531 36.539062 1.600539e-04 *
JN.1.38.1 107 15 7.072920 -9.326679 36.653357 1.514886e-04 *
LP.8.1.5 168 15 7.027250 -25.461006 68.922012 1.489493e-11
JN.1 17255 13 6.967998 6.095705 5.808589 7.537042e+02 * *
|||||

XEC.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 17 261.385774 NaN NaN NaN * * *
XEC.6 45 2 259.683711 259.423336 -226.846671 1.561287e-06
XEC.31 66 17 249.414537 260.838102 -229.676204 6.427017e-06 *
XEC.15 127 2 247.771080 248.556135 -205.112270 2.969626e-11
XEC.24 11 17 247.354286 258.823653 -225.647306 8.568525e-07 *
XEC.29 135 15 247.155609 252.455289 -212.910577 1.467068e-09
XEC.2.2 273 21 245.924553 240.926408 -189.852816 1.442231e-14
XEC.2 921 6 243.179137 235.579887 -179.159775 6.882257e-17
XEC.8 592 17 242.121633 253.469042 -214.938084 4.048174e-09 *
XEC.2.1 265 17 241.983075 237.093317 -182.186633 3.131028e-16 *



Target sequence

, 54_T|A, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4930_T|C, 6183_A|G, 7165_C|T, 7842_A|G, 8247_C|T, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21578_G|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21844_C|T,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25452_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IVY-G25Y94R9/2025


Target: 5350 samples Number of changes: 142
BC: XEC.2 + XEC.18 + XEC.2BC BR: 3-4, 15-16 BC BR coord: 896 - 897, 7841 - 7842
Direction L1: << Initial region span: 1-3,5-15,16-142Gap history (edge excluded): 3-16 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.32e-02
Rec. model vs L1: 1.29e-30Rec. model vs L2: 3.16e-20
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 3 4.681558 None None None * * *
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 5 14.256531 NaN NaN NaN * * *
LF.7.9.3 20 14 9.958902 -25.945726 87.891452 7.661374e-14
XEC.24 11 5 8.798033 -1.201967 38.403935 4.274877e-03 * *
LF.7.3.5 16 14 7.173478 -28.508007 93.016013 5.893066e-15
LF.7.9 20 14 6.963170 -28.823675 93.647351 4.300694e-15
PC.3.1 27 14 6.663065 -37.730533 111.461066 5.836415e-19
JN.1.41 121 14 6.549406 -11.185720 58.371441 1.970122e-07
XBB.1.5.97 39 15 6.349111 -60.422937 156.845874 8.125178e-29
B.1.474 13 15 6.349111 -106.473793 248.947586 8.139018e-49
GN.1.4 13 15 6.349111 -69.934752 175.869503 6.021329e-33
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 279.381372 NaN NaN NaN * * *
XEC.18 165 5 266.714506 257.164636 -248.329272 2.077201e-12
XEC.24 11 5 261.309602 257.230389 -248.460778 2.216703e-12
XEC.31 66 16 258.670168 263.358453 -260.716905 1.018434e-09 *
XEC.29 135 16 258.229842 262.948662 -259.897323 6.758838e-10 *
XEC.9 305 16 258.101204 262.783680 -259.567361 5.730776e-10 *
XEC.28 39 16 258.027638 262.667838 -259.335677 5.108220e-10 *
XEC.19 59 16 257.776717 262.443350 -258.886701 4.078996e-10 *
XEC.14 193 16 257.738993 262.431674 -258.863348 4.018268e-10 *
XEC.17 13 16 256.741368 261.460188 -256.920375 1.523257e-10 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1218_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3482_G|A, 3565_T|C, 4184_G|A, 4321_C|T, 5926_T|C, 6183_A|G, 7834_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22927_G|T, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25435_T|C, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IVY-G25Y98H5/2025


Target: 5350 samples Number of changes: 143
BC: XEC.15 + XEC.2 BC BR: 5-6 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-5,7-143Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.97e-19 Rec. model vs L2: 7.14e-16
Flags: Model_2BP_Bad_L1_opp

XEC.15 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.15 127 5 12.808072 NaN NaN NaN * * *
XEC.30 135 5 12.017272 12.017272 -12.034545 4.515812e-01 * *
XEC.39 155 5 11.912143 11.912143 -11.824285 4.065697e-01 * *
NM.2 28 4 10.652217 0.652217 10.695567 5.235752e-06 *
LP.7 57 4 10.477981 0.477981 11.044038 4.417220e-06 *
KP.2.24 44 4 9.583943 -0.416057 12.832113 1.804910e-06 *
MC.14 35 4 9.377846 -0.622154 13.244308 1.470365e-06 *
KP.2.3.13 25 4 8.568321 -1.431679 14.863359 6.541037e-07 *
JN.1.1.6 13 4 8.123635 -9.120888 30.241775 2.991727e-10 *
KP.3.4 62 4 7.931484 -2.068516 16.137033 3.449039e-07 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 268.083499 NaN NaN NaN * * *
XEC.8 592 2 259.645691 248.721177 -203.442354 8.567067e-05 *
XEC.36 30 2 250.053785 239.048565 -184.097130 5.410091e-09
XEC.17 13 2 241.820527 230.815307 -167.630613 1.434794e-12
XEC.14 193 7 241.797265 231.797265 -169.594529 3.822945e-12 *
XEC.2.2 273 15 240.070471 226.209990 -158.419980 1.435038e-14
XEC.31 66 15 238.670168 224.805821 -155.611642 3.521110e-15
XEC.32 42 2 238.577431 227.572211 -161.144422 5.591185e-14
XEC.29 135 15 238.229842 218.284521 -142.569041 5.188952e-18
MC.24.1 25 2 238.172992 227.862520 -161.725039 7.509668e-14



Target sequence

, 106_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2433_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6500_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16443_C|T, 17410_C|T,
18163_A|G, 18492_A|G, 18632_T|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22388_C|T, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22639_C|A, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/IVY-G25Z06J6/2025


Target: 5350 samples Number of changes: 151
BC: XEC.33 + XEC.2 BC BR: 13-14 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-13,33-151Gap history (edge excluded): 13-33
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 6.60e-01
Rec. model vs L1: 8.07e-34Rec. model vs L2: 3.96e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 13 17.494146 NaN NaN NaN * * *
KP.3.1.1 12013 13 14.119344 14.119344 3.761311 3.421812e-02 * *
XEC.4.1.1 12 4 11.005220 -3.039664 38.079328 1.207154e-09
XEC.25 13 4 11.005220 5.079158 21.841683 4.057271e-06
XEC.4.1.4 23 4 11.005220 0.008634 31.982731 2.548948e-08
XEC.36 30 4 11.005220 5.045257 21.909486 3.917723e-06
XEC.32 42 4 11.005220 5.079158 21.841683 4.057271e-06
XEC.3 29 4 11.005220 5.044067 21.911866 3.917723e-06
XEC.29 135 4 11.005220 -0.377024 32.754048 1.734433e-08
XEC.27 25 4 11.005220 4.995777 22.008446 3.726653e-06
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 33 231.429180 NaN NaN NaN * * *
XEC.39 155 46 225.103290 155.636125 -19.272251 3.062670e-21
XEC.31 66 46 218.124388 148.670168 -5.340337 2.892272e-24
XEC.40 52 46 218.110565 142.331001 7.337998 5.102841e-27
XEK.1 88 46 217.996332 149.523285 -7.046571 6.800813e-24
XEC.2.1 265 46 217.810630 138.650357 14.699285 1.287088e-28
XEC.25 13 46 217.720550 141.724358 8.551285 2.786531e-27
XEC.29 135 46 217.698932 149.602211 -7.204421 7.330489e-24
XEK.5 28 46 217.603736 137.364286 17.271427 3.560738e-29
XEC.33 169 46 217.580545 140.350438 11.299124 7.045454e-28



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2069_A|G, 2790_C|T, 2847_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7125_C|A, 7842_A|G, 8293_C|T, 8393_G|A, 8991_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10663_T|C, 11042_G|T, 11139_C|T, 11288_11296, 11727_G|A, 12213_C|T, 12427_T|C, 12781_C|T, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15763_C|T, 17274_C|T, 17410_C|T, 18060_C|T, 18086_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G,
21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25669_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27795_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/LA-CDC-2-8448566/2025


Target: 5350 samples Number of changes: 146
BC: XEC.9 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-9,13-146Gap history (edge excluded): 9-13
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.51e-16 Rec. model vs L2: 7.29e-24
Flags: Model_2BP_Bad_L1_opp

XEC.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.9 305 9 20.521588 NaN NaN NaN * * *
KP.3.3 1715 12 17.382156 17.382156 -10.764313 111.608811 *
XEC.18 165 12 13.785538 13.785538 -3.571076 3.064854 *
XEC.15 127 12 12.887384 12.887384 -1.774768 1.246077 *
MC.24 831 9 12.803342 4.947791 14.104418 0.000446 * *
KP.3.1 1957 9 11.763566 3.906842 16.186315 0.000157 * *
KP.3.1.1 12013 12 11.308495 11.308495 1.383010 0.257947 *
LF.7.4 15 4 10.108672 0.429719 23.140563 0.000005
XEC.32 42 9 9.322509 1.469367 21.061265 0.000014 * *
XEC.16 23 9 9.322509 1.469367 21.061265 0.000014 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 13 221.423823 NaN NaN NaN * * *
XEC.15 127 3 218.746493 195.863675 -105.727350 7.932919e-12
XEC.9 305 40 217.415245 194.405749 -102.811498 1.842312e-12
XEC.33 169 40 217.217325 192.518706 -99.037413 2.797164e-13
XEC.2.1 265 40 217.060504 190.430079 -94.860158 3.459733e-14
XEC.2.2 273 40 215.821498 203.772860 -121.545721 2.161237e-08
XEC.13 30 40 213.552422 196.566633 -107.133266 1.597494e-11
XEC.8 592 37 211.038611 199.432561 -112.865121 2.817503e-10
XEC.18 165 3 207.347002 183.566030 -81.132060 3.610862e-17
XEC.31 66 40 206.714596 189.797799 -93.595599 1.842625e-14



Target sequence

, 241_C|T, 521_523, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3653_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
9803_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11908_A|G, 12529_A|G, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13426_C|T, 14408_C|T, 15538_G|A,
15714_C|T, 15756_T|A, 16293_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21057_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25267_C|T,
25584_C|T, 25658_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/LA-CDC-LC1137035/2025


Target: 5350 samples Number of changes: 141
BC: KP.2.5 + XEC.14 BC BR: 3-4 BC BR coord: 678 - 679
Direction L1: << Initial region span: 1-3,5-141Gap history (edge excluded): 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.80e-138Rec. model vs L2: 1.66e-17
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.5 66 3 9.391444 NaN NaN NaN * * *
CM.3 22 3 6.639909 6.639909 -7.279818 0.063928 * *
BQ.1.1.7 1146 4 6.349948 2.677297 0.645407 0.001213 * *
KP.5 77 3 6.000082 6.000082 -6.000164 0.033709 * *
BN.1.2.3 117 3 5.653341 5.653341 -5.306682 0.023873 * *
BQ.1.26 121 3 5.611641 5.611641 -5.223282 0.022823 * *
BA.5.2.48 267 3 5.234796 5.234796 -4.469593 0.015686 * *
BF.7.24 444 3 4.319240 4.319240 -2.638479 0.006282 * *
BQ.1.11 1938 3 3.937737 3.937737 -1.875474 0.004296 * *
BF.3 355 3 3.844681 3.844681 -1.689363 0.003907 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 265.924099 NaN NaN NaN * * *
XEK.1 88 17 263.493156 202.362097 -96.724194 5.457781e-24
XEC.2.2 273 17 261.614127 225.577593 -143.155185 6.627259e-14
XEC.31 66 17 261.301202 237.335343 -166.670685 8.442393e-09
XEC.29 135 17 260.860876 230.829310 -153.658620 1.262932e-11
XEC.9 305 17 260.732237 249.719111 -191.438222 2.019309e-03 *
XEC.28 39 17 260.658672 237.593207 -167.186414 1.094919e-08
XEC.19 59 17 260.407751 237.555495 -167.110989 1.051987e-08
XEC.2 921 17 260.352396 220.158678 -132.317356 2.933985e-16
XEC.8 592 5 259.445082 249.445082 -190.890165 1.533811e-03 * *



Target sequence

, 241_C|T, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6411_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MA-MASPHL-13857/2025


Target: 5350 samples Number of changes: 145
BC: XEC.2 + JN.1.4 BC BR: 134-135 BC BR coord: 28271 - 28272
Direction L1: >> Initial region span: 1-134,135-145Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 6.64e-28 Rec. model vs L2: 1.23e-40
Flags: Model_2BP_Bad_L1_opp

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 134 239.094108 NaN NaN NaN * * *
MC.24.1 25 140 215.448660 208.647334 -133.294669 5.966684e-14
XEC.25 13 134 213.044929 213.044929 -142.089858 4.859916e-12 *
XEC.9 305 134 210.992612 210.992612 -137.985223 6.256408e-13 *
KP.3.3 1715 134 209.495652 209.495652 -134.991304 1.395993e-13 *
KP.2 1589 140 205.753893 199.057093 -114.114186 4.081774e-18
XEC.18 165 134 205.121870 205.121870 -126.243739 1.757296e-15 *
XEC.24 11 134 205.084947 205.084947 -126.169895 1.696855e-15 *
XEC.36 30 134 205.002307 205.002307 -126.004613 1.558582e-15 *
XEC.17 13 134 204.856962 204.856962 -125.713924 1.348208e-15 *
|||||

JN.1.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.4 8971 135 8.824759 NaN NaN NaN * * *
XBB.1.6 63 143 7.701175 -19.105800 66.211599 7.415751e-13
KP.3.1.1 12013 135 7.486499 7.486499 13.027002 2.618457e-01 * *
GN.1.2 14 143 6.780777 -20.100305 68.200610 2.741777e-13
FL.21.2 11 143 6.569954 -24.200491 76.400982 4.543858e-15
JN.1.4.5 1757 142 6.358146 3.108803 21.782394 3.296151e-03 *
CB.1 82 143 6.308325 -20.523342 69.046684 1.792491e-13
BA.2.47 679 142 6.044353 -10.777386 49.554773 3.074880e-09
LZ.1.1 18 143 6.026834 -16.469150 60.938301 1.034001e-11
BU.2 67 143 6.016630 -23.834289 75.668578 6.545491e-15



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 679_C|T, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5822_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11546_A|G, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14514_T|C, 15651_T|C, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21875_A|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22347_C|T, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29212_G|A, 29479_T|C, 29510_A|C, 29670_C|T, 29734_29759

Case 72 (XEC): USA/MA-MASPHL-13878/2025


Target: 5350 samples Number of changes: 146
BC: XEC.31 + JN.1.1 + XEC.31BC BR: 10-11, 38-39 BC BR coord: 3566 - 3567, 15590 - 15591
Direction L1: << Initial region span: 1-10,11-30,39-146Gap history (edge excluded): 10-39 -> 30-39
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.36e-18
Rec. model vs L1: 1.20e-27 Rec. model vs L2: 1.01e-73
Flags: Model_2BP_Best

XEC.31 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.31 66 10 23.393083 None None None * * *
|||||

JN.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.1 3081 30 28.676856 NaN NaN NaN * * *
JN.1.13.1 751 36 20.906996 0.906996 68.186008 7.228963e-07
JN.1.8.1 1498 30 19.265047 4.667079 60.665842 3.104726e-05 * *
MC.10.1 650 30 18.299583 -16.204617 102.409234 2.681004e-14 *
JN.1 17255 36 17.872708 17.404804 35.190392 1.059095e+01 *
JN.1.4 8971 36 17.711033 9.920049 50.159903 5.946217e-03 *
KP.3.1.1 12013 34 16.845862 9.661502 50.676995 4.584840e-03 *
KP.2.2 1334 36 14.772792 -5.227208 80.454417 1.573442e-09
KP.2.3 4440 36 14.513041 4.129563 61.740875 1.818343e-05 *
KV.2 236 15 14.209157 -19.308873 108.617746 1.201747e-15
|||||

XEC.31 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.31 66 39 246.096884 NaN NaN NaN * * *
XEC.2.2 273 39 245.650945 253.813632 -267.627264 1.557521e-07 *
XEC.9 305 39 244.700294 268.105049 -296.210099 2.503238e-01 * *
XEC.18 165 39 238.974479 262.276532 -284.553065 7.354706e-04 * *
XEC.33 169 32 238.970357 256.022860 -272.045719 1.419792e-06
XEC.39 155 39 238.163561 260.707696 -281.415392 1.537781e-04 * *
XEC.40 52 43 238.110565 256.875311 -273.750623 3.321812e-06
XEK.1 88 43 237.996332 239.734737 -239.469473 1.195550e-13
XEC.2.1 265 43 237.810630 240.690964 -241.381927 3.106840e-13
XEC.25 13 43 237.720550 254.819385 -269.638770 4.255004e-07



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6353_T|C, 7842_A|G, 8290_C|T, 8293_C|T, 8393_G|A, 8860_C|T,
9344_C|T, 9424_A|G, 9534_C|T, 9967_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12757_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15042_T|C, 15588_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17502_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MA-MASPHL-13989/2025


Target: 5350 samples Number of changes: 149
BC: XEC.19 + KP.2.3 + XEC.19BC BR: 9-10, 15-16 BC BR coord: 3566 - 3567, 6899 - 6900
Direction L1: << Initial region span: 1-9,10-15,16-149Gap history (edge excluded): 9-16 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.96e-14
Rec. model vs L1: 3.43e-20 Rec. model vs L2: 8.02e-82
Flags: Model_2BP_Best

XEC.19 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.19 59 9 19.453239 None None None * * *
|||||

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 15 8.729715 NaN NaN NaN * * *
MC.36 49 12 8.538252 -7.851957 41.703915 6.300826e-08
LU.2.1.1 49 12 8.538252 -14.304510 54.609019 9.908927e-11
XBB.1.5.86 101 12 7.814951 -22.185049 70.370097 3.747884e-14
FL.13 151 12 7.399459 -35.879717 97.759433 4.227885e-20
XBB.2.3 695 11 6.202173 -35.285736 96.571472 7.665286e-20
BA.1.21.1 65 10 6.108827 -48.037197 122.074395 2.224712e-25
KP.3.1.1 12013 14 5.992641 5.502703 14.994593 3.975578e-02 * *
BA.5.1.2 2225 12 5.408043 -17.996531 61.993061 2.474457e-12
EG.5.1.4 1717 12 4.978238 -29.441046 84.882091 2.648376e-17
|||||

XEC.19 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.19 59 16 215.078272 NaN NaN NaN * * *
XEC.29 135 16 212.613878 233.603918 -159.207835 3.965314e-01 * *
XEC.2 921 14 210.878415 212.337568 -116.675136 2.306776e-10
XEC.14 193 16 208.923291 229.599654 -151.199308 7.226503e-03 * *
XEC.8 592 1 205.591952 219.268660 -130.537320 2.358665e-07
XEC.40 52 16 205.362088 225.966571 -143.933143 1.906636e-04 * *
XEC.39 155 16 203.865924 224.225056 -140.450111 3.346535e-05 * *
KP.3.1.1 12013 1 202.976380 197.473676 -86.947352 8.076403e-17
XEC.9 305 1 200.893179 213.908285 -119.816570 1.108786e-09
KP.3.3 1715 16 199.390583 211.340453 -114.680905 8.486155e-11 *



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3754_A|G, 4184_G|A, 4321_C|T, 5175_C|T, 6183_A|G, 6896_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10456_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13043_G|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19875_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23262_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25234_G|A, 25429_G|T,
25584_C|T, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27630_C|A, 27807_C|T,
27810_T|C, 28254, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MI-MDHHS-SC45757/2025


Target: 5350 samples Number of changes: 142
BC: KP.3.1.1 + XEC.19 BC BR: 14-15 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-14,16-142Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.57e-01
Rec. model vs L1: 1.86e-73Rec. model vs L2: 2.83e-16
Flags: Model_1BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 14 14.895823 NaN NaN NaN * * *
XEC.18 165 12 13.579186 7.188977 19.622046 4.505687e-04 *
JN.1.42.1 18 4 10.232834 -14.057470 62.114939 2.674082e-13
JN.1.61 13 4 9.516802 -6.489302 46.978605 5.159558e-10
BA.2.86.2 74 4 8.876299 -34.321045 102.642090 4.228605e-22
KP.3.1 1957 14 8.727667 8.727667 16.544667 2.101718e-03 * *
JN.1.67 32 4 8.616016 -7.310046 48.620093 2.272433e-10
JN.1.18.3 97 4 7.507040 -8.527824 51.055648 6.708907e-11
PP.1 127 4 7.172964 -21.065694 76.131387 2.414184e-16
JN.1.7.5 427 4 7.064239 1.991836 30.016329 2.485591e-06
|||||

XEC.19 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.19 59 16 260.283476 NaN NaN NaN * * *
XEC.4 192 6 255.079262 244.761483 -221.522966 3.985869e-03 *
XEC.14.1 14 6 253.984259 243.623920 -219.247840 1.281146e-03 *
XEC.31 66 16 247.089186 237.089186 -206.178373 1.859877e-06 *
XEC.29 135 16 246.648860 228.085783 -188.171565 2.283823e-10 *
XEC.9 305 16 246.520222 230.437406 -192.874813 2.394719e-09 *
XEC.14 193 6 246.502684 236.158011 -204.316021 7.338215e-07
XEC.28 39 16 246.446656 236.446656 -204.893313 9.758080e-07 *
XEC.2 921 16 246.133855 236.133855 -204.267710 7.157034e-07 *
XEC.17 13 6 245.520726 235.160386 -202.320773 2.699579e-07



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1347_C|T, 1549_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4927_C|T, 6183_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19170_C|A, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27600_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29046_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MI-UM-10063263439/2025


Target: 5350 samples Number of changes: 151
BC: XEC.8 + XEC.2 BC BR: 13-14 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-11,16-151Gap history (edge excluded): 11-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 5.83e-03
Rec. model vs L1: 3.82e-31Rec. model vs L2: 1.29e-12
Flags: Model_1BP_Best

XEC.8 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 11 26.139423 NaN NaN NaN * * *
KP.3.3 1715 13 20.929997 20.929997 -15.859993 3.254374e+00 *
XEC.18 165 14 20.707592 17.110728 -8.221456 7.136127e-02 *
XEC.33 169 14 20.642463 17.045455 -8.090910 6.687032e-02 *
MC.24 831 13 19.806993 19.806993 -13.613986 1.056541e+00 *
KP.3.1.1 12013 13 16.574239 16.574239 -7.148477 4.179410e-02 *
XEC.9 305 13 16.449763 16.449763 -6.899526 3.688317e-02 *
XEC.16 23 15 13.603314 5.079158 15.841683 4.255004e-07
JN.1.8.1 1498 14 11.990692 8.388417 9.223166 1.165238e-05 *
JN.1 17255 14 11.476711 7.874986 10.250028 6.962305e-06
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 246.921343 NaN NaN NaN * * *
XEC.8 592 1 201.070379 181.321165 -62.642329 1.939078e-26
XEC.2.2 273 13 200.028422 196.418630 -92.837261 7.005544e-20
KP.3.1.1 12013 1 195.448802 178.874563 -57.749127 1.681687e-27
XEC.18 165 5 187.838093 165.434026 -30.868053 2.448090e-33
XEC.40 52 16 184.390794 177.993737 -55.987475 6.975351e-28 *
KP.3.3 1715 1 179.631975 158.701979 -17.403957 2.909739e-36
JN.1 17255 6 178.389892 164.989949 -29.979898 1.568795e-33
XEC.29 135 16 178.007347 163.047212 -26.094425 2.243177e-34 *
XEC.9 305 5 174.577957 152.810670 -5.621341 8.051180e-39



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1387_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4754_C|T, 6183_A|G, 7842_A|G, 8074_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10702_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13968_C|T, 14408_C|T, 15540_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19728_T|C, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22224_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25668_A|G, 26058_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26832_G|T, 26833_C|T, 26858_C|T, 27084_G|T, 27107_A|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29499_A|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MN-MDH-46757/2025


Target: 5350 samples Number of changes: 147
BC: XEC.32 + BR.3 + XEC.32BC BR: 5-6, 9-10 BC BR coord: 2060 - 2061, 3430 - 3431
Direction L1: << Initial region span: 1-3,6-9,10-147Gap history (edge excluded): 3-10 -> 3-6
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.19e-07
Rec. model vs L1: 6.38e-15Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 3 4.718819 None None None * * *
|||||

BR.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BR.3 23 6 9.952023 NaN NaN NaN * * *
B.1.568 466 7 8.694898 -1.305102 12.610205 1.294242e-05 * *
GS.1 109 6 8.676527 8.676527 -7.353054 2.794310e-01 * *
XBB.1.5.52 654 6 8.080372 8.080372 -6.160744 1.541237e-01 * *
GJ.3 25 8 6.941899 -1.980893 13.961786 6.589718e-06
BA.4.1.2 19 8 6.941899 -1.980893 13.961786 6.589718e-06
XBB.1.3 10 8 5.737926 -3.184866 16.369732 1.974886e-06
LP.8.1 1124 6 5.683011 5.683011 -1.366022 1.405187e-02 * *
B.1.36.9 152 8 5.009061 -22.064144 54.128289 1.247562e-14
XBB.1.5.59 284 6 4.969515 4.969515 0.060970 6.874063e-03 * *
|||||

XEC.32 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 10 230.184908 NaN NaN NaN * * *
XEC.8 592 8 225.447391 224.204075 -138.408150 9.256633e-04 *
XEC.9 305 10 224.875219 225.844096 -141.688192 4.771951e-03 * *
XEC.2 921 8 222.287797 206.852916 -103.705832 2.700498e-11
XEC.18 165 10 217.703982 218.690965 -127.381929 3.726653e-06 *
KP.3.3 1715 8 216.503013 220.881331 -131.762663 3.329844e-05 *
XEC.14 193 10 210.716170 211.695253 -113.390506 3.415302e-09 *
XEC.29 135 15 210.702025 210.680829 -111.361658 1.237714e-09
XEC.17 13 10 209.734212 210.739433 -111.478865 1.314250e-09 *
XEC.15 127 10 207.439707 208.429054 -106.858108 1.304541e-10 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1513_C|T, 2060_G|A, 2790_C|T, 2918_C|T, 3037_C|T, 3176_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12436_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13711_A|G, 14408_C|T, 15714_C|T, 15756_T|A,
16323_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22329_C|T, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22792_C|T, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23896_C|T, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25766_T|C, 26060_C|T, 26270_C|T, 26510_T|C, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/MT-MTPHL-4166796/2025


Target: 5350 samples Number of changes: 141
BC: XEC.4.6 + XEC.2 BC BR: 3-4 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-3,4-141Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.84e-42 Rec. model vs L2: 3.74e-09
Flags: Model_2BP_Bad_L1_opp

XEC.4.6 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.6 10 3 7.272505 NaN NaN NaN * * *
XEC.4.6.1 13 3 3.917565 3.917565 0.164870 0.034909 * *
XEC.19 59 3 3.802697 3.802697 0.394607 0.031117 * *
XEC.28 39 3 3.777179 3.777179 0.445642 0.030197 * *
XEC.6 45 3 3.772984 3.772984 0.454033 0.030197 * *
XEC.15 127 3 3.766384 3.766384 0.467232 0.029897 * *
XEC.4 192 3 3.766259 3.766259 0.467482 0.029897 * *
XEC.4.1 68 3 3.765326 3.765326 0.469348 0.029897 * *
XEC.33 169 3 3.762595 3.762595 0.474811 0.029897 * *
XEC.8 592 3 3.756099 3.756099 0.487802 0.029599 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 4 244.566822 NaN NaN NaN * * *
KP.3.3 1715 3 222.915227 221.185623 -142.371245 7.017703e-11 *
XEC.8 592 3 222.902776 216.628270 -133.256540 7.378764e-13 *
XEC.14 193 3 221.147457 214.861056 -129.722113 1.256847e-13 *
XEC.19 59 3 219.947967 213.661566 -127.323132 3.785550e-14 *
XEC.4 192 3 216.365937 210.079536 -120.159071 1.055249e-15 *
XEC.9 305 3 215.046790 208.760389 -117.520779 2.818942e-16 *
XEC.33 169 3 214.779127 208.498660 -116.997320 2.173549e-16 *
XEC.13 30 3 213.989807 207.703405 -115.406811 9.815341e-17 *
XEC.39 155 3 213.666943 207.387014 -114.774029 7.127400e-17 *



Target sequence

, 241_C|T, 670_T|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15177_A|T, 15714_C|T, 15756_T|A, 17410_C|T, 18131_C|T, 18163_A|G,
18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21774_C|T, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22624_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24865_C|T, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25139_T|C, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/NC-CDC-LC1136794/2025


Target: 5350 samples Number of changes: 142
BC: MC.24 + XEC.2 BC BR: 13-14 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-13,15-142Gap history (edge excluded): 13-15
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.82e-118Rec. model vs L2: 5.39e-21
Flags: Model_2BP_Bad_L1_opp

MC.24 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.24 831 13 12.224416 NaN NaN NaN * * *
MC.6 366 4 9.223728 -3.937710 43.875419 9.541787e-08
CQ.1 92 3 7.678656 -59.033676 154.067351 1.127652e-31
BQ.1.1.67 297 3 6.510885 -63.994790 163.989580 7.908144e-34
BQ.1.1.5 1362 3 5.676021 -51.796692 139.593384 1.572053e-28
KS.1.3 45 13 5.226691 5.226691 25.546617 9.118820e-04 * *
XEC.25 13 13 5.079158 5.079158 25.841683 7.887982e-04 * *
XEC.18.3 13 13 5.079158 5.079158 25.841683 7.887982e-04 * *
XEC.32 42 13 5.079158 5.079158 25.841683 7.887982e-04 * *
XEC.22 23 13 5.079158 5.079158 25.841683 7.887982e-04 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 265.162474 NaN NaN NaN * * *
XEC.36 30 4 259.769990 245.816197 -217.632395 8.740134e-05 *
XEC.38 34 4 259.579917 245.652848 -217.305695 7.447850e-05 *
XEC.29 135 15 259.430411 240.867333 -207.734667 6.190994e-07 *
XEC.31 66 15 258.976919 248.976919 -223.953839 2.060102e-03 * *
XEC.32 42 4 258.937850 244.950156 -215.900312 3.680047e-05 *
XEC.13 30 4 258.227125 244.273333 -214.546666 1.873719e-05 *
XEK.1 88 22 258.080150 239.567712 -205.135423 1.695700e-07
XEK.5 28 22 257.040926 238.528488 -203.056975 5.993531e-08
XEC.9 305 15 256.877298 240.794482 -207.588965 5.772445e-07 *



Target sequence

, 241_C|T, 670_T|G, 885_G|T, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3246_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7480_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18743_A|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY12004/2025


Target: 5350 samples Number of changes: 141
BC: KP.2.5 + XEC.14 BC BR: 3-4 BC BR coord: 678 - 679
Direction L1: << Initial region span: 1-3,5-141Gap history (edge excluded): 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.13e-145Rec. model vs L2: 1.66e-17
Flags: Model_2BP_Bad_L1_opp

KP.2.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.5 66 3 9.391444 NaN NaN NaN * * *
CM.3 22 3 6.639909 6.639909 -7.279818 0.063928 * *
BQ.1.1.7 1146 4 6.349948 2.677297 0.645407 0.001213 * *
KP.5 77 3 6.000082 6.000082 -6.000164 0.033709 * *
BN.1.2.3 117 3 5.653341 5.653341 -5.306682 0.023873 * *
BQ.1.26 121 3 5.611641 5.611641 -5.223282 0.022823 * *
BA.5.2.48 267 3 5.234796 5.234796 -4.469593 0.015686 * *
BF.7.24 444 3 4.319240 4.319240 -2.638479 0.006282 * *
BQ.1.11 1938 3 3.937737 3.937737 -1.875474 0.004296 * *
BF.3 355 3 3.844681 3.844681 -1.689363 0.003907 * *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 276.499648 NaN NaN NaN * * *
XEC.8 592 5 271.990858 261.990858 -225.981716 1.099846e-02 * *
XEC.9 305 5 269.837039 259.837039 -221.674078 1.274757e-03 * *
XEC.3 29 8 264.226759 254.140514 -210.281029 4.286672e-06
XEC.13 30 8 262.691703 252.605458 -207.210917 9.235878e-07
XEC.29 135 16 261.793841 241.762275 -185.524550 1.801169e-11
XEC.2 921 16 261.562400 231.368682 -164.737365 5.536494e-16
XEC.18 165 8 259.889050 249.790648 -201.581295 5.532727e-08
XEC.33 169 8 257.721668 247.605535 -197.211071 6.223085e-09
XEC.30 135 8 256.872574 246.748818 -195.497635 2.646574e-09



Target sequence

, 241_C|T, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6912_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NMDOH-2025013208/2025


Target: 5350 samples Number of changes: 145
BC: KP.3.1.1 + XEC.27 BC BR: 15-16 BC BR coord: 7367 - 7368
Direction L1: << Initial region span: 1-12,16-145Gap history (edge excluded): 12-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.14e-55 Rec. model vs L2: 2.03e-08
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 12 12.481728 NaN NaN NaN * * *
XEC.19 59 11 12.093654 -21.084319 92.168638 1.210073e-08 *
JN.1.8.1 1498 12 7.534864 -11.976290 73.952579 1.094547e-04 * *
PD.2.1 10 3 7.171233 -51.357525 152.715049 8.600945e-22
XEC.32 42 14 6.995760 -3.004240 56.008481 8.607080e-01 *
KP.2.2 1334 12 6.656877 -12.688307 75.376614 5.354436e-05 * *
JN.1.7.8 34 3 5.902722 -36.516483 123.032967 2.407952e-15
JN.1.11 43 3 5.583160 -30.464071 110.928141 1.021244e-12
BQ.1.1.18 1989 4 5.425645 -45.601394 141.202788 2.729495e-19
JN.1 17255 12 4.574337 0.945412 48.109176 4.470118e+01 * *
|||||

XEC.27 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.27 25 16 211.414459 NaN NaN NaN * * *
XEC.2 921 16 203.967771 203.967771 -125.935542 5.843561e-04 * *
XEC.32 42 5 203.021342 183.489692 -84.979384 7.452922e-13
XEK.5 28 16 201.087826 201.087826 -120.175651 3.280269e-05 * *
KP.3.3 1715 15 197.635552 196.601549 -111.203097 3.680673e-07 *
XEC.15 127 16 194.812415 194.812415 -107.624830 6.145258e-08 *
XEC.29 135 16 194.314388 194.314388 -106.628776 3.745971e-08 *
XEC.9 305 16 194.082834 194.082834 -106.165668 2.976299e-08 *
XEC.14 193 16 193.474180 193.474180 -104.948361 1.617175e-08 *
XEC.31 66 16 189.834481 189.834481 -97.668962 4.245463e-10 *



Target sequence

, 241_C|T, 670_T|G, 897_C|G, 1148_G|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6362_G|A, 7318_C|T, 7360_G|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15162_A|G, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18186_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22893_A|C, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25324_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28851_G|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29134_G|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-CDC-LC1135259/2025


Target: 5350 samples Number of changes: 147
BC: KP.3.3 + KS.1 + KP.3.3BC BR: 6-7, 16-17 BC BR coord: 2060 - 2061, 7118 - 7119
Direction L1: << Initial region span: 1-6,7-15,17-147Gap history (edge excluded): 6-17 -> 15-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.07e-02
Rec. model vs L1: 1.23e-21Rec. model vs L2: 4.75e-90
Flags: Model_2BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 6 7.681506 None None None * * *
|||||

KS.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1 505 15 19.327580 NaN NaN NaN * * *
KP.3.1.1 12013 16 15.830678 11.444617 19.110766 8.289586e+00 * *
MC.19 221 11 14.033159 -4.597003 51.194006 8.962916e-07
XEC.11.1 166 11 12.714431 -19.879797 81.759593 2.061855e-13
JN.1.32 436 11 11.706616 -2.545936 47.091871 6.962305e-06
MC.10.1 650 11 11.319780 -7.311921 56.623843 5.933895e-08
XEK.1 88 10 9.687591 -29.726620 101.453240 1.093022e-17
JN.1 17255 11 9.428992 -4.824643 51.649287 7.121338e-07
JN.3 321 10 8.393487 -22.187899 86.375797 2.046623e-14
BL.1.3 10 9 8.287639 -60.142726 162.285453 6.720334e-31
|||||

KP.3.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 17 240.659483 NaN NaN NaN * * *
XEC.14 193 13 238.986499 231.297759 -174.595518 3.977608e-08
XEC.6 45 13 235.908261 214.763895 -141.527791 2.621578e-15
XEC.33 169 32 226.386729 224.576511 -161.153022 4.775201e-11
XEC.2.1 265 32 226.166983 194.579219 -101.158437 4.490851e-24
XEC.8 592 17 220.315464 220.758603 -153.517207 1.052345e-12 *
XEK.6 23 24 219.180173 189.773365 -91.546730 3.677424e-26
XEC.31 66 17 218.670168 209.644854 -131.289707 1.566661e-17 *
XEC.29 135 17 218.229842 209.235063 -130.470125 1.039715e-17 *
XEC.9 305 17 218.101204 209.070081 -130.140163 8.815678e-18 *



Target sequence

, 241_C|T, 337_C|T, 556_C|T, 670_T|G, 897_C|A, 2060_G|A, 2526_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4113_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6218_T|C, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 9923_G|A, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12053_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21897_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24912_C|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25460_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28153_C|T,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-CDC-LC1136530/2025


Target: 5350 samples Number of changes: 144
BC: BQ.1.1.7 + XEC.8 BC BR: 5-6 BC BR coord: 874 - 875
Direction L1: << Initial region span: 1-5,6-144Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.51e-18
Flags: Model_2BP_Bad_L1_opp

BQ.1.1.7 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BQ.1.1.7 1146 5 7.593118 NaN NaN NaN * * *
BF.7.24 444 4 5.257856 -4.742144 23.484288 4.395189e-06 *
BQ.1.11 1938 4 4.655529 -5.344471 24.688942 2.400100e-06 *
JN.1.22 516 4 4.257580 -5.742420 25.484840 1.616900e-06 *
BA.2.86.1 1343 4 4.060345 -5.939655 25.879310 1.323806e-06 *
AY.43.9 285 3 3.744530 -16.255470 46.510940 4.386081e-11
XBB.1.5.21 611 4 3.730621 -6.269379 26.538758 9.517152e-07 *
XFG.3 480 4 3.720497 -6.279503 26.559005 9.422455e-07 *
BQ.1 15159 4 3.542165 -6.457835 26.915670 7.870296e-07 *
BA.2.8 4985 4 2.995111 -7.004889 28.009777 4.563526e-07 *
|||||

XEC.8 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.8 592 6 263.956456 NaN NaN NaN * * *
XEC.14 193 6 256.499648 256.499648 -212.999296 5.785417e-04 * *
XEC.2 921 17 252.616041 232.422324 -164.844647 2.016153e-14
XEC.29 135 18 251.793841 231.762275 -163.524550 1.042051e-14
XEC.9 305 18 250.850166 249.837039 -199.674078 7.374998e-07
XEC.3 29 18 250.187912 244.140514 -188.281029 2.480018e-09
XEC.13 30 18 248.651666 242.605458 -185.210917 5.343340e-10
XEC.30 135 9 248.236963 248.113206 -196.226412 1.320613e-07
XEC.17 13 9 247.151054 247.064810 -194.129620 4.621322e-08
XEC.18 165 18 245.833461 239.790648 -179.581295 3.200913e-11



Target sequence

, 241_C|T, 516_518, 592_T|C, 670_T|G, 875_C|A, 897_C|A, 2060_G|A, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6912_A|G, 7765_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11020_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25987_G|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-CDC-LC1136873/2025


Target: 5350 samples Number of changes: 147
BC: XEC.9 + XEC.2 BC BR: 6-7 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-6,8-147Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.68e-01
Rec. model vs L1: 1.59e+01Rec. model vs L2: 5.85e-16
Flags: Model_1BP_Best

XEC.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.9 305 6 13.156712 NaN NaN NaN * * *
MV.1 127 4 10.771135 -9.228865 30.457729 1.898095e-10
MV.2 21 4 10.746124 -9.253876 30.507753 1.851231e-10
MB.1.1.1 53 4 10.634215 -9.365785 30.731570 1.658396e-10
MM.1 35 5 10.514447 0.514447 10.971107 3.239797e-06 *
LF.7.6 15 4 10.389449 -9.610551 31.221103 1.298034e-10
MH.1 51 4 9.400665 -10.599335 33.198670 4.823192e-11
MC.29 54 4 7.904542 -12.095458 36.190916 1.081594e-11
MD.1 19 4 7.850475 -12.149525 36.299050 1.023713e-11
LF.1.1.1 109 4 7.647881 -12.352119 36.704239 8.381452e-12
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 8 239.758565 NaN NaN NaN * * *
XEC.8 592 8 237.711377 227.711377 -153.422754 1.287349e-01 * *
XEC.14 193 8 237.384176 227.384176 -152.768351 9.301449e-02 * *
XEC.29 135 8 234.072747 224.072747 -146.145495 3.396533e-03 * *
XEC.32 42 8 231.497436 221.497436 -140.994873 2.573689e-04 * *
XEC.9 305 1 231.383122 218.226410 -134.452820 9.781673e-06
XEC.31 66 8 230.316550 220.316550 -138.633101 7.908400e-05 * *
XEC.6 45 8 228.154591 218.154591 -134.309181 9.120372e-06 *
XEC.25 13 5 225.912519 214.233238 -126.466476 1.809582e-07
XEC.30 135 8 224.898591 214.898591 -127.797182 3.518714e-07 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2177_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25096_C|T, 25207_C|T, 25584_C|T, 25810_C|T,
26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-NYCPHL-019769/2025


Target: 5350 samples Number of changes: 140
BC: BA.5.1.30 + XEC.2 BC BR: 4-5 BC BR coord: 672 - 673
Direction L1: << Initial region span: 1-4,7-140Gap history (edge excluded): 4-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 2.60e-10
Flags: Model_2BP_Bad_L1_opp

BA.5.1.30 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
BA.5.1.30 4775 4 2.782144 NaN NaN NaN * * *
B.1.243 5209 3 2.218682 -7.781318 23.562636 0.000026 * *
B.1.258 3961 3 2.077191 -7.922809 23.845617 0.000022 * *
BA.2 443141 4 1.613450 1.613450 4.773100 0.311923 * *
BA.2.9 75328 4 1.443566 1.443566 5.112868 0.263158 * *
BA.5.6 14873 4 1.204625 1.204625 5.590750 0.207008 * *
BA.5.1 53705 4 0.653552 0.653552 6.692895 0.119433 * *
BQ.1.1 36940 4 0.483196 0.483196 7.033608 0.100761 * *
B.1.1.7 477665 3 0.192926 -9.807074 27.614149 0.000003 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 283.039884 NaN NaN NaN * * *
XEC.33 169 4 261.294403 260.213439 -222.426878 7.284004e-08
XEC.8 592 4 260.304259 259.243025 -220.486050 2.761242e-08
KP.3.3 1715 4 260.291054 259.214706 -220.429413 2.679635e-08
XEC.39 155 4 259.526352 258.445925 -218.891851 1.240706e-08
XEC.2.1 265 15 258.853734 248.663436 -199.326872 7.018898e-13
XEC.14 193 5 255.648685 247.805866 -197.611733 2.970131e-13
XEC.4 192 4 251.954063 250.867164 -203.734328 6.334565e-12
XEC.38 34 4 251.845531 250.788486 -203.576971 5.876851e-12
XEC.17 13 4 251.298389 250.211491 -202.422981 3.290439e-12



Target sequence

, 241_C|T, 508_T|C, 642_A|G, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6941_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21777_G|A, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C,
29733_29758, 29759_G|T

Case 72 (XEC): USA/NY-PRL-250318_81E02/2025


Target: 5350 samples Number of changes: 142
BC: XEC.18.3 + XEC.2 BC BR: 12-13 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-12,14-142Gap history (edge excluded): 12-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.70e-01
Rec. model vs L1: 2.18e-46Rec. model vs L2: 1.05e-17
Flags: Model_1BP_Best

XEC.18.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18.3 13 12 15.079158 NaN NaN NaN * * *
XEC.22 23 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.24 11 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.25 13 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.4.3 10 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.16 23 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.17 13 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.32 42 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.4.1 68 12 15.049528 15.049528 -6.099057 0.970446 * *
XEC.13 30 12 15.045257 15.045257 -6.090514 0.965605 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 14 242.784986 NaN NaN NaN * * *
XEC.6 45 5 238.591404 218.322530 -156.645061 5.249305e-07
XEC.9 305 5 238.395407 218.081910 -156.163820 4.108655e-07
XEC.8 592 5 238.391667 218.084474 -156.168948 4.129249e-07
KP.3.3 1715 5 237.583410 221.818211 -163.636423 1.729661e-05 *
XEC.30 135 5 236.488199 216.226930 -152.453861 6.428111e-08
XEC.39 155 5 234.839354 214.524750 -149.049500 1.174310e-08
XEC.14 193 5 234.451604 214.106931 -148.213862 7.715767e-09
XEC.33 169 5 234.450387 214.138066 -148.276132 7.990600e-09
XEC.38 34 5 229.679604 209.379889 -138.759778 6.844436e-11



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1117_T|C, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6547_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G,
18555_C|T, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21599_21610, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21969_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25855_G|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-PRL-250318_81E03/2025


Target: 5350 samples Number of changes: 140
BC: XBC.1.3.1 + XEC.14 BC BR: 4-5 BC BR coord: 686 - 687
Direction L1: << Initial region span: 1-4,5-140Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 9.94e-20
Flags: Model_2BP_Bad_L1_opp

XBC.1.3.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XBC.1.3.1 13 4 9.312302 NaN NaN NaN * * *
BA.4.1.11 107 4 8.829163 8.829163 -9.658327 0.618783 * *
NL.2.1 16 4 7.653830 7.653830 -7.307660 0.191092 * *
BA.4.8 14 4 7.084645 7.084645 -6.169289 0.108067 * *
BA.4.1.9 194 4 6.927847 6.927847 -5.855694 0.092551 * *
DC.1 59 4 6.801790 6.801790 -5.603581 0.081268 * *
BA.4.6.1 399 4 5.960023 5.960023 -3.920046 0.035084 * *
NL.2 237 4 5.913637 5.913637 -3.827273 0.033541 * *
NL.15 13 3 5.881306 -4.118694 16.237388 0.000001 *
NL.14 12 3 5.881306 -4.118694 16.237388 0.000001 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 5 280.259967 NaN NaN NaN * * *
XEC.9 305 1 274.632388 273.404643 -254.809286 1.054172e-03 *
XEC.30 135 5 271.506529 271.506529 -251.013059 1.576710e-04 * *
XEC.33 169 3 268.403155 267.842439 -243.684878 4.037035e-06
XEC.38 34 3 264.754147 263.306958 -234.613916 4.330490e-08
XEC.4 192 1 263.872900 263.203786 -234.407573 3.918390e-08
XEC.19 59 1 263.209301 261.566566 -231.133132 7.600894e-09
XEC.17 13 5 262.851212 262.851212 -233.702425 2.747471e-08 *
XEC.16 23 1 261.776075 258.249253 -224.498507 2.761712e-10
XEC.25 13 3 261.125888 257.994287 -223.988574 2.140097e-10



Target sequence

, 241_C|T, 509_523, 670_T|G, 686_694, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5806_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15026_C|T, 15714_C|T, 15756_T|A, 17078_A|G,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-PRL-250325_82H02/2025


Target: 5350 samples Number of changes: 141
BC: XEC.2 + XEC.25 + XEC.2BC BR: 4-5, 6-7 BC BR coord: 941 - 942, 2789 - 2790
Direction L1: << Initial region span: 1-3,5-6,7-141Gap history (edge excluded): 3-7 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.59e-02
Rec. model vs L1: 5.00e-17Rec. model vs L2: 5.21e-25
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 3 4.681558 None None None * * *
|||||

XEC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.25 13 5 11.679280 NaN NaN NaN * * *
XEC.9 305 4 8.474236 7.425306 -10.850612 1.419309e-02 * *
XEC.4 192 5 7.888122 7.888122 -11.776244 2.259560e-02 * *
XEC.8 592 5 7.443363 7.443363 -10.886727 1.447981e-02 * *
XEC.18.3 13 6 6.286401 -3.713599 11.427198 2.060803e-07 *
XEC.28 39 6 6.286401 -3.713599 11.427198 2.060803e-07 *
XEC.4.1.4 23 6 6.286401 -3.713599 11.427198 2.060803e-07 *
XEC.4.1 68 6 6.286401 -3.713599 11.427198 2.060803e-07 *
XEC.38 34 6 6.286401 -3.713599 11.427198 2.060803e-07 *
XEC.36 30 6 6.286401 -3.713599 11.427198 2.060803e-07 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 222.193476 NaN NaN NaN * * *
XEC.9 305 1 220.891895 213.466589 -114.933178 3.175644e-06
XEC.8 592 5 215.678685 202.885329 -93.770658 8.072280e-11
XEC.31 66 6 213.915344 202.317227 -92.634454 4.565080e-11 *
XEC.14 193 6 213.879702 213.099387 -114.198774 2.204522e-06 *
KP.3.3 1715 1 213.087069 211.945417 -111.890834 6.945512e-07
XEC.15 127 6 210.046975 198.463519 -84.927039 9.714370e-13 *
XEC.6 45 6 204.645884 193.055830 -74.111659 4.343917e-15 *
XEC.32 42 6 203.927310 192.359728 -72.719457 2.167938e-15 *
XEC.30 135 6 202.522072 190.962207 -69.924413 5.346069e-16 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A, 16887_C|T,
17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21610_T|C, 21641_G|T, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994,
22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25810_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-PRL-250401_82H04/2025


Target: 5350 samples Number of changes: 140
BC: XEC.2 + B.1.561 + XEC.2BC BR: 10-11, 13-14 BC BR coord: 4330 - 4331, 6182 - 6183
Direction L1: << Initial region span: 1-10,11-13,14-140Gap history (edge excluded): 10-14 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.98e-06
Rec. model vs L1: 9.48e-25 Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 10 5.098043 None None None * * *
|||||

B.1.561 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
B.1.561 1058 11 10.280817 NaN NaN NaN * * *
AY.94 218 13 6.229347 -13.770653 37.541307 3.591019e-11
B.1.558 181 12 5.536276 -4.463724 18.927449 3.947552e-07 *
FY.1 23 13 5.220251 -14.779749 39.559498 1.307917e-11
B.1.1.50 79 13 5.084910 -24.133193 58.266385 1.131763e-15
AY.20 12743 11 3.657758 3.657758 2.684485 1.333431e-03 * *
MK.1 151 13 3.338465 -16.661535 43.323069 1.995752e-12
LP.8.1.1 2345 13 2.792929 -4.310545 18.621089 4.609391e-07
BQ.1.8 1899 12 1.751395 0.624919 8.750162 6.410424e-05 * *
AY.4.6 9691 13 1.479377 -4.957839 19.915678 2.406313e-07
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 14 270.890862 NaN NaN NaN * * *
XEC.30 135 1 265.285409 284.461224 -278.922448 4.769515e+03 *
XEC.39 155 14 262.790929 284.208089 -278.416178 3.714502e+03 * *
XEC.18 165 14 260.586715 282.019496 -274.038993 4.157150e+02 * *
XEC.14 193 3 258.524785 279.144285 -268.288570 2.345304e+01 *
XEC.19 59 14 258.028613 279.445795 -268.891589 3.165829e+01 * *
XEC.29 135 19 255.570629 271.104945 -252.209890 7.559124e-03 *
XEK.5 28 19 255.506468 252.480483 -214.960966 6.162213e-11
XEC.9 305 19 255.471357 273.425111 -256.850222 7.691918e-02 *
XEC.31 66 14 254.695317 276.118882 -262.237763 1.138828e+00 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4456_C|T, 5512_C|T, 5999_A|G, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 8655_C|T, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 18912_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A,
29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-PRL-250422_82D10/2025


Target: 5350 samples Number of changes: 146
BC: XEC.9 + XEC.2 BC BR: 6-7 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-6,8-146Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.68e-01
Rec. model vs L1: 1.65e+01Rec. model vs L2: 5.82e-16
Flags: Model_1BP_Best

XEC.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.9 305 6 13.156712 NaN NaN NaN * * *
MV.1 127 4 10.771135 -9.228865 30.457729 1.898095e-10
MV.2 21 4 10.746124 -9.253876 30.507753 1.851231e-10
MB.1.1.1 53 4 10.634215 -9.365785 30.731570 1.658396e-10
MM.1 35 5 10.514447 0.514447 10.971107 3.239797e-06 *
LF.7.6 15 4 10.389449 -9.610551 31.221103 1.298034e-10
MH.1 51 4 9.400665 -10.599335 33.198670 4.823192e-11
MC.29 54 4 7.904542 -12.095458 36.190916 1.081594e-11
MD.1 19 4 7.850475 -12.149525 36.299050 1.023713e-11
LF.1.1.1 109 4 7.647881 -12.352119 36.704239 8.381452e-12
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 8 236.127429 NaN NaN NaN * * *
XEC.8 592 8 234.200121 224.200121 -144.400243 1.458758e-01 * *
XEC.14 193 8 233.752114 223.752114 -143.504228 9.301449e-02 * *
XEC.29 135 8 230.454130 220.454130 -136.908259 3.447865e-03 * *
XEC.9 305 1 227.793871 214.637159 -125.274317 1.023190e-05 *
XEC.6 45 8 224.525821 214.525821 -125.051641 9.166088e-06 *
XEC.32 42 8 223.927888 213.927888 -123.855776 5.055671e-06 *
XEC.31 66 8 222.731908 212.731908 -121.463815 1.522739e-06 *
XEC.30 135 8 221.354081 211.354081 -118.708163 3.850087e-07 *
KP.3.3 1715 8 220.933277 210.933277 -117.866554 2.529687e-07 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 936_C|T, 1102_C|T, 2060_G|A, 2177_G|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15219_A|G, 15360_C|T, 15714_C|T, 15756_T|A,
16887_C|T, 17410_C|T, 18163_A|G, 18490_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25096_C|T, 25207_C|T, 25584_C|T, 25810_C|T, 26060_C|T, 26093_A|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27654_C|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/NY-PRL-250506_81E06/2025


Target: 5350 samples Number of changes: 141
BC: KP.3.3 + XEC.2 BC BR: 14-15 BC BR coord: 6806 - 6807
Direction L1: << Initial region span: 1-14,15-141Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.35e-01
Rec. model vs L1: 6.20e-29Rec. model vs L2: 3.56e-21
Flags: Model_1BP_Best

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 14 23.967811 NaN NaN NaN * * *
KP.3.1.1 12013 14 16.681795 16.681795 2.636410 6.823281e-04 * *
XEC.27 25 7 15.661018 -5.004223 46.008446 2.608059e-13
XEC.4.1.4 23 7 15.661018 -16.646216 69.292432 2.296834e-18
XEC.8.1 12 7 15.661018 -5.007853 46.015706 2.595051e-13
XEC.36 30 7 15.661018 -4.954743 45.909486 2.741777e-13
XEC.32 42 7 15.661018 -4.920842 45.841683 2.839438e-13
XEC.13 30 7 15.661018 -4.954743 45.909486 2.741777e-13
XEC.3 29 7 15.661018 -4.955933 45.911866 2.741777e-13
XEC.29 135 7 15.661018 -18.940102 73.880203 2.314322e-19
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 275.190515 NaN NaN NaN * * *
XEC.14 193 15 269.660996 269.660996 -267.321992 3.965989e-03 * *
XEC.8 592 15 268.822922 268.822922 -265.645843 1.720741e-03 * *
XEC.18 165 11 267.325535 258.482620 -244.965240 5.560459e-08
XEC.28 39 15 256.483069 256.483069 -240.966138 7.525264e-09 *
XEC.4.3 10 15 255.318638 245.906523 -219.813046 1.912873e-13 *
XEC.9 305 15 255.087002 249.004187 -226.008373 4.246186e-12 *
KP.3.3 1715 1 253.089716 229.121905 -186.243809 9.818683e-21
XEC.4 192 15 251.816343 251.816343 -231.632687 7.052880e-11 *
XEK.1 88 26 246.667131 241.297117 -210.594235 1.903656e-15



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3433_G|A, 3565_T|C, 3688_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 6794_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10582_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28603_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/OK-CDC-2-8448976/2025


Target: 5350 samples Number of changes: 142
BC: JN.1.38 + XEC.2 BC BR: 13-14 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-13,15-142Gap history (edge excluded): 13-15
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 7.38e-09
Rec. model vs L1: 1.34e-112Rec. model vs L2: 1.40e-21
Flags: Model_1BP_Best

JN.1.38 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.38 247 13 23.844392 NaN NaN NaN * * *
JN.1.18 431 13 23.358963 23.358963 -14.717926 6.156972e-01 * *
JN.1.9 576 13 22.162810 22.162810 -12.325620 1.863740e-01 * *
JN.1 17255 13 20.813196 20.813196 -9.626392 4.831564e-02 * *
BA.2.86.1 1343 13 20.598213 20.598213 -9.196426 3.896856e-02 * *
JN.1.45 268 10 19.003710 16.208954 -0.417907 4.832386e-04 *
MC.13 807 12 18.983062 18.199194 -4.398388 3.535148e-03 * *
MC.40 21 10 18.817432 11.643355 8.713290 5.030456e-06
XEC.2.6 13 10 18.623899 8.017767 15.964466 1.340571e-07
JN.1.5 174 10 18.432058 13.317145 5.365710 2.672262e-05 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 260.483777 NaN NaN NaN * * *
XEC.30 135 15 247.270755 237.270755 -202.541510 1.823049e-06 *
XEC.9 305 15 244.297465 234.297465 -196.594929 9.306199e-08 *
XEK.5 28 25 244.139319 229.553173 -187.106347 8.132358e-10
XEC.2.2 273 25 243.474717 227.666603 -183.333206 1.228570e-10
XEC.13 30 15 242.101942 232.101942 -192.203885 1.036325e-08 *
XEC.8 592 15 238.625867 228.625867 -185.251734 3.208652e-10 *
XEC.39 155 15 237.278104 227.278104 -182.556208 8.359813e-11 *
XEC.31 66 5 235.978142 222.891816 -173.783633 1.036678e-12
XEC.29 135 15 233.278671 223.278671 -174.557342 1.531153e-12 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2485_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5672_C|T, 6183_A|G, 7842_A|G, 8157_C|T, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11005_C|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15951_C|T, 16887_C|T,
17410_C|T, 18163_A|G, 18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20703_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/OK-CDC-2-8506526/2025


Target: 5350 samples Number of changes: 143
BC: XEC.15 + XEC.2 BC BR: 13-14 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-10,14-143Gap history (edge excluded): 10-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.47e-07
Rec. model vs L1: 2.58e-16Rec. model vs L2: 1.53e-24
Flags: Model_1BP_Best

XEC.15 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.15 127 10 12.064195 NaN NaN NaN * * *
XEC.5 126 10 11.428839 3.559696 28.880607 5.220458e-01 * *
KP.3.1.1 12013 10 11.301197 3.446806 29.106387 4.653339e-01 * *
MC.9 298 4 9.587999 -9.999051 55.998101 6.740241e-07
MC.13 807 4 9.291477 -10.277047 56.554093 5.119699e-07
MC.11 393 4 9.290290 -10.284216 56.568432 5.068757e-07
LF.4.1 50 3 4.718819 -29.546164 95.092328 2.189726e-15
LB.1.3.3 22 3 4.718819 -24.817034 85.634067 2.480862e-13
LD.1.1 11 3 4.718819 -43.530791 123.061582 1.848338e-21
LD.2 13 3 4.718819 -49.801673 135.603346 3.497478e-24
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 14 249.259018 NaN NaN NaN * * *
KP.3.3 1715 8 244.758422 234.888416 -187.776831 5.743654e-07
XEC.8 592 12 244.573331 242.428163 -202.856327 1.080858e-03 *
XEC.33 169 31 243.012472 232.285952 -182.571905 4.244741e-08
XEC.2.1 265 31 242.855651 238.985469 -195.970939 3.448452e-05 *
XEC.14 193 12 240.191495 238.044637 -194.089274 1.347061e-05 *
XEC.13 30 12 236.933225 234.786367 -187.572733 5.171153e-07
XEC.18 165 31 236.889053 233.938277 -185.876554 2.221307e-07
XEC.29 135 15 235.836792 225.449683 -168.899367 4.565080e-11 *
XEC.4 192 12 235.346048 233.199190 -184.398380 1.059816e-07



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1976_G|A, 2060_G|A, 2790_C|T, 2937_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4092_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 9724_C|T, 10029_C|T, 10198_C|T, 10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11967_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24023_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25003_A|G, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/OSPHL10236/2025


Target: 5350 samples Number of changes: 142
BC: XEC.30 + XEC.2 BC BR: 13-14 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-13,16-142Gap history (edge excluded): 13-16
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.84e-15 Rec. model vs L2: 1.65e-24
Flags: Model_2BP_Bad_L1_opp

XEC.30 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.30 135 13 18.227570 NaN NaN NaN * * *
XEC.33 169 13 17.353324 17.353324 -0.706648 4.168620e-01 * *
XEC.35.1 28 13 16.529119 16.529119 0.941762 1.826835e-01 * *
KP.3.1.1 12013 13 14.058814 14.058814 5.882372 1.545226e-02 * *
JN.1.2 650 13 12.025764 12.025764 9.948472 2.019309e-03 * *
XEC.27 25 14 11.845144 4.995777 24.008446 1.786951e-06 *
MC.1 932 13 9.774387 9.774387 14.451227 2.128336e-04 * *
KP.2.2 1334 13 9.740843 9.740843 14.518314 2.055133e-04 * *
NV.1 13 4 9.635840 -20.581855 75.163711 1.396469e-17
KP.3.3 1715 13 9.558425 9.558425 14.883150 1.716591e-04 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 254.645226 NaN NaN NaN * * *
XEC.8 592 6 247.877542 227.570350 -181.140699 8.459926e-04 *
XEC.31 66 16 246.188008 226.188008 -178.376017 2.128336e-04 * *
XEC.9 305 16 245.757797 219.674982 -165.349964 3.152184e-07 *
XEC.28 39 16 245.722025 225.722025 -177.444049 1.330215e-04 * *
XEC.29 135 16 245.681045 217.117967 -160.235935 2.449002e-08 *
XEC.14 193 6 245.674335 225.329662 -176.659324 9.006310e-05 *
XEC.19 59 16 245.468024 225.468024 -176.936048 1.035972e-04 * *
XEC.17 13 6 244.461986 224.101646 -174.203293 2.632478e-05 *
XEC.2.3 28 16 243.530331 215.172045 -156.344090 3.484295e-09 *



Target sequence

, 241_C|T, 344_C|T, 670_T|G, 897_C|A, 1281_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6334_T|C, 7385_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26078_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28511_C|T, 28639_C|A, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 72 (XEC): USA/PA-CDC-LC1136045/2025


Target: 5350 samples Number of changes: 143
BC: XEC.29 + XEC.39 BC BR: 11-12 BC BR coord: 4330 - 4331
Direction L1: << Initial region span: 1-11,18-143Gap history (edge excluded): 11-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 6.54e-01
Rec. model vs L1: 2.29e-15Rec. model vs L2: 3.66e-07
Flags: Model_1BP_Best

XEC.29 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.29 135 11 24.521489 NaN NaN NaN * * *
XEC.9 305 11 22.952481 22.952481 -21.904962 2.080452e-01 * *
XEC.5 126 13 15.744161 11.405366 1.189268 2.014781e-06
KP.3.1.1 12013 13 15.671634 12.108195 -0.216389 4.077608e-06
XEC.30 135 13 15.617739 11.347936 1.304127 1.906960e-06
MC.24 831 11 15.235110 15.235110 -6.470219 9.280593e-05 * *
XEC.8 592 13 14.832127 11.347409 1.305181 1.897449e-06
KP.3.1 1957 11 13.501014 13.501014 -3.002028 1.637098e-05 * *
KP.2.15 253 13 12.593569 7.569547 8.860906 4.352197e-08
XEC.11 16 13 12.300046 5.897558 12.204885 8.192883e-09
|||||

XEC.39 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.39 155 18 258.151444 NaN NaN NaN * * *
KP.3.3 1715 18 256.051133 227.003390 -170.006780 5.181010e+00 * *
XEC.31 66 18 255.067225 222.279959 -160.559919 4.595926e-02 * *
XEC.2.1 265 18 254.687825 214.074118 -144.148235 1.255992e-05 * *
XEC.29 135 18 254.626899 207.842734 -131.685468 2.473615e-08 *
XEC.9 305 18 254.498261 215.628180 -147.256359 5.947229e-05 * *
XEC.28 39 18 254.424695 214.662889 -145.325779 2.265794e-05 * *
XEC.19 59 18 254.173774 214.598744 -145.197488 2.123202e-05 * *
XEC.14 193 18 254.136049 221.348784 -158.697567 1.813340e-02 * *
XEC.2 921 18 254.112980 226.521723 -169.043447 3.189933e+00 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2462_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5869_C|T, 6183_A|G, 6402_C|T, 6693_A|G, 7842_A|G, 8140_C|T, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10870_G|T, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29461_T|C, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11147/2025


Target: 5350 samples Number of changes: 145
BC: XEC.33 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,16-145Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01
Rec. model vs L1: 5.46e-32Rec. model vs L2: 3.98e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 14 17.783166 NaN NaN NaN * * *
XEC.4 192 14 17.681102 17.681102 -3.362204 9.003245e-01 * *
XEC.16 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.4.3 10 12 15.079158 -7.384864 46.769728 1.171677e-11
XEC.32 42 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.17 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.22 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.18.3 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.24 11 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.25 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 271.351893 NaN NaN NaN * * *
XEC.14 193 28 245.024085 230.424664 -184.849328 3.710592e-14
XEC.29 135 16 242.299684 232.299684 -188.599368 2.419610e-13 *
XEC.25 13 28 237.617708 216.556357 -157.112714 3.513813e-20
XEC.30 135 28 234.867262 220.260406 -164.520813 1.428367e-18
XEC.2.1 265 28 229.985151 205.687253 -135.374506 6.683403e-25
XEC.5 126 28 227.124600 212.525180 -149.050360 6.245568e-22
XEC.18 165 28 226.505286 211.905866 -147.811731 3.359768e-22
XEC.9 305 24 225.734380 215.706172 -155.412344 1.501856e-20
XEC.39 155 5 223.777073 209.859526 -143.719052 4.346875e-23



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T,
26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/PA-CDC-LC1136147/2025


Target: 5350 samples Number of changes: 143
BC: JN.1 + XEC.2 BC BR: 23-24 BC BR coord: 11047 - 11048
Direction L1: << Initial region span: 1-23,25-143Gap history (edge excluded): 23-25
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 8.38e-04
Rec. model vs L1: 5.50e-37Rec. model vs L2: 2.27e-15
Flags: Model_1BP_Best

JN.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 23 38.964896 NaN NaN NaN * * *
JN.1.20 66 21 37.160733 30.749040 -7.498080 2.705645e-04 *
JN.1.7.5 427 23 35.922361 35.922361 -17.844722 4.759631e-02 * *
JN.1.13.1 751 21 34.713774 28.302081 -2.604161 2.334798e-05 *
LF.4 38 23 33.218853 33.218853 -12.437707 3.198735e-03 * *
JN.1.4 8971 23 32.984622 32.984622 -11.969244 2.528826e-03 * *
KP.1.1 593 21 32.870851 26.459158 1.081684 3.708066e-06
LB.1.3.1 292 23 32.739976 32.739976 -11.479952 1.979324e-03 * *
JN.1.4.6 167 21 31.945957 25.534263 2.931473 1.470365e-06
XDY.3 16 13 27.833353 7.413717 39.172567 1.986137e-14
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 25 248.985986 NaN NaN NaN * * *
XEC.9 305 4 239.296957 218.982638 -189.965275 2.061154e-09
XEC.8 592 4 239.081990 226.050856 -204.101712 2.412131e-06
XEC.29 135 25 234.694456 224.694456 -201.388913 6.222026e-07 *
XEC.18 165 40 233.975527 206.282372 -164.564745 6.257473e-15
XEC.4 192 40 233.775322 206.076946 -164.153891 5.097633e-15
XEK.5 28 25 232.964077 222.964077 -197.928154 1.103068e-07 *
XEC.2.2 273 25 232.209266 222.209266 -196.418532 5.184538e-08 *
XEC.39 155 4 227.394284 214.362558 -180.725116 2.030813e-11
XEC.31 66 40 227.359801 209.973397 -171.946794 2.518356e-13



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9120_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11005_C|T, 11042_G|T, 11243_G|A, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15951_C|T, 16887_C|T, 17410_C|T,
18109_C|T, 18163_A|G, 18395_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26029_C|A, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/SC-CDC-2-8448555/2025


Target: 5350 samples Number of changes: 144
BC: KS.1.1.1 + XEC.13 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,10-144Gap history (edge excluded): 4-10
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 5.21e-147Rec. model vs L2: 5.92e-09
Flags: Model_2BP_Bad_L1_opp

KS.1.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KS.1.1.1 20 4 13.218879 NaN NaN NaN * * *
JN.1.53 62 4 11.072687 11.072687 -14.145374 0.117068 * *
KP.3.1.3 46 4 10.134678 10.134678 -12.269355 0.045730 * *
JN.1.21 60 4 9.852167 9.852167 -11.704335 0.034390 * *
KR.1 62 4 9.026165 9.026165 -10.052329 0.015071 * *
KP.2.3.3 149 4 8.155586 8.155586 -8.311173 0.006314 * *
NY.15 216 4 7.866899 7.866899 -7.733798 0.004724 * *
KP.3.2.3 759 4 7.676542 7.676542 -7.353083 0.003907 * *
JN.1.16.1 466 4 7.084762 7.084762 -6.169525 0.002166 * *
NY.13 463 4 7.071031 7.071031 -6.142063 0.002133 * *
|||||

XEC.13 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.13 30 10 260.771155 NaN NaN NaN * * *
XEC.2 921 10 254.284706 225.364714 -146.729428 1.285118e-10 *
XEC.14 193 10 251.084775 238.452271 -172.904541 6.189940e-05 * *
XEC.8 592 10 250.518260 237.873860 -171.747721 3.483110e-05 * *
KP.3.3 1715 10 245.519445 228.327809 -152.655618 2.492449e-09 *
XEC.40 52 10 235.248580 214.979366 -125.958732 3.970041e-15 *
XEC.25 13 10 233.442831 220.810326 -137.620652 1.351238e-12 *
XEC.4 192 10 232.866614 220.234109 -136.468218 7.603481e-13 *
XEC.36 30 10 232.239472 219.606968 -135.213935 4.049552e-13 *
XEC.28 39 10 231.672960 219.014479 -134.028958 2.244777e-13 *



Target sequence

, 241_C|T, 599_G|A, 670_T|G, 897_C|A, 1567_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3354_G|A, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18449_G|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20811_T|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25571_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26625_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29296_C|T, 29510_A|C, 29700_A|G

Case 72 (XEC): USA/SC-CDC-LC1134656/2025


Target: 5350 samples Number of changes: 141
BC: XEC.18 + XEC.27 BC BR: 131-132 BC BR coord: 28311 - 28312
Direction L1: >> Initial region span: 1-131,133-141Gap history (edge excluded): 131-133
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.62e-17 Rec. model vs L2: 2.87e-44
Flags: Model_2BP_Bad_L1_opp

XEC.18 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 131 271.688833 NaN NaN NaN * * *
XEC.8 592 141 268.317616 265.146982 -256.293964 1.437284e-03 *
XEC.30 135 138 263.288840 262.725065 -251.450130 1.278056e-04 *
XEC.24 11 131 260.788452 260.788452 -247.576903 1.845823e-05 * *
XEC.36 30 138 260.613602 260.004365 -246.008729 8.419164e-06
XEC.2 921 141 260.553750 257.833657 -241.667314 9.612801e-07
XEC.17 13 138 259.424370 258.815133 -243.630265 2.561289e-06
XEC.32 42 138 256.181274 255.572037 -237.144074 9.980975e-08
MC.24.1 25 131 256.095961 256.095961 -238.191921 1.687243e-07 *
XEC.4 192 138 255.591885 255.008924 -236.017848 5.701223e-08
|||||

XEC.27 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.27 25 133 17.509500 NaN NaN NaN * * *
XEC.40 52 133 17.289559 7.289559 5.420882 0.802519 * *
PG.4 14 133 16.831188 6.831188 6.337624 0.506617 * *
XEC.15 127 133 15.487799 5.487799 9.024402 0.132655 * *
KP.3.3 1715 133 14.754545 4.754545 10.490911 0.063609 * *
XEC.2.1 265 133 14.696635 4.696635 10.606729 0.059905 * *
KP.3.3.3 288 133 14.512208 4.512208 10.975585 0.049787 * *
KP.3.3.4 292 133 13.929129 3.929129 12.141742 0.027876 * *
XEC.8 592 133 13.170634 3.170634 13.658732 0.013037 * *
XEC.2 921 133 12.720093 2.720093 14.559813 0.008312 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10078_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17339_C|T, 17410_C|T, 18163_A|G, 18492_A|G,
18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T,
26846_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28329_G|A, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29421_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/SD-CDC-2-8398256/2025


Target: 5350 samples Number of changes: 145
BC: JN.1.59 + XEC.14 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-145Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.22e-105Rec. model vs L2: 9.13e-16
Flags: Model_2BP_Bad_L1_opp

JN.1.59 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.59 77 4 6.038966 NaN NaN NaN * * *
JN.1.7 1974 4 4.716446 4.716446 -1.432892 2.658030e-01 * *
KP.2 1589 4 3.002048 3.002048 1.995904 4.783489e-02 * *
LB.1.7 1971 4 2.791065 2.791065 2.417870 3.877421e-02 * *
BF.7.24 444 3 2.063169 -7.936831 23.873662 8.525790e-07 *
BQ.1.1.7 1146 3 1.807521 -8.192479 24.384959 6.606775e-07 *
JN.1 17255 4 1.715084 1.715084 4.569833 1.323355e-02 * *
BA.2.3.2 372 3 1.534247 -8.465753 24.931506 5.018322e-07 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 6 240.295382 NaN NaN NaN * * *
XEC.4 192 6 239.727092 229.727092 -153.454184 5.655254e-01 * *
XEC.9 305 6 234.491446 224.491446 -142.982892 3.012455e-03 * *
XEC.33 169 6 232.632946 222.632946 -139.265893 4.713074e-04 * *
XEC.2 921 15 230.378687 206.576245 -107.152490 4.994993e-11
XEC.17 13 6 227.101708 217.101708 -128.203415 1.859877e-06 *
XEC.2.2 273 15 226.754570 194.754347 -83.508695 3.674296e-16
XEC.15 127 6 226.032571 216.032571 -126.065142 6.411515e-07 *
XEC.2.1 265 36 225.453383 196.765848 -87.531697 2.742244e-15
KP.3.3 1715 4 224.481700 220.880935 -135.761870 8.149246e-05 *



Target sequence

, 241_C|T, 670_T|G, 733_T|C, 897_C|A, 1348_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7644_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11124_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14646_T|G, 14868_T|C, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19324_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20436_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25655_T|C,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/TN-CDC-LC1135518/2025


Target: 5350 samples Number of changes: 145
BC: XEC.4.3 + XEC.2 BC BR: 11-12 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-8,13-145Gap history (edge excluded): 8-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.76e-02
Rec. model vs L1: 4.38e-36Rec. model vs L2: 1.07e-17
Flags: Model_1BP_Best

XEC.4.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.3 10 8 19.322509 NaN NaN NaN * * *
XEC.17 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.18.3 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.4.1.4 23 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.16 23 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.22 23 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.24 11 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.25 13 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.8.1 12 8 19.322509 11.469367 -0.938735 1.0 * *
XEC.32 42 8 19.322509 11.469367 -0.938735 1.0 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 13 242.091895 NaN NaN NaN * * *
XEC.14 193 3 231.964442 221.623149 -155.246297 2.851729e-05 *
XEC.13 30 1 231.121914 219.686448 -151.372897 4.098047e-06
XEC.15 127 1 230.572144 219.200663 -150.401327 2.523156e-06
XEC.29 135 14 228.813573 208.426465 -128.852930 5.277413e-11 *
XEC.4 192 1 227.715782 216.304723 -144.609446 1.395281e-07
XEC.30 135 1 224.844883 213.496946 -138.993893 8.400287e-09
XEC.2.1 265 13 221.487393 211.487393 -134.974787 1.125543e-09 *
XEC.32 42 1 220.173020 208.703653 -129.407306 6.982703e-11
XEC.33 169 28 218.514240 204.157655 -120.315309 7.415751e-13



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3871_G|C, 4184_G|A, 4321_C|T, 5720_G|A, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10323_A|G, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11530_C|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15735_T|C, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19493_G|A, 19716_C|T, 19955_C|T, 20055_A|G, 20555_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29095_C|T, 29409_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): USA/TN-SPHL-1120/2025


Target: 5350 samples Number of changes: 146
BC: KP.3.3 + KP.2.2 BC BR: 142-143 BC BR coord: 28883 - 28884
Direction L1: >> Initial region span: 1-137,143-146Gap history (edge excluded): 137-143
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 7.77e-06 Rec. model vs L2: 1.25e-91
Flags: Model_2BP_Bad_L1_opp

KP.3.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 137 230.577621 NaN NaN NaN * * *
XEC.8 592 143 224.941378 221.333078 -138.666156 4.274877e-03 *
XEC.32 42 143 219.836446 216.228146 -128.456292 2.593285e-05 *
XEC.33 169 137 218.993436 215.209734 -126.419468 9.351255e-06 *
XEC.4 192 137 218.547775 214.743732 -125.487465 5.873852e-06 *
XEC.31 66 137 218.028254 214.235219 -124.470439 3.527222e-06 *
XEC.14 193 143 214.782719 211.174419 -118.348837 1.653833e-07
XEC.24 11 137 211.567155 201.586271 -99.172541 1.131378e-11 *
XEC.18 165 137 211.024563 201.565082 -99.130165 1.108975e-11 *
XEC.36 30 137 210.783068 207.005301 -110.010603 2.555546e-09 *
|||||

KP.2.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.2 1334 143 9.703448 NaN NaN NaN * * *
BE.5 231 144 7.942662 -2.057338 12.114676 7.810825e-06 *
XEC.32 42 138 5.881863 -3.995542 15.991085 1.122446e-06
BQ.1.10 2048 144 5.637057 -4.362943 16.725885 7.753122e-07 *
BQ.1.1 36940 144 5.577032 -0.638570 9.277141 3.215315e-05 * *
CH.1.1 4056 144 5.057243 -4.942757 17.885514 4.340961e-07 *
XEC.14 193 138 4.241647 -4.110738 16.221476 1.000511e-06
BA.4.1 18821 144 4.219795 -2.014633 12.029266 8.129591e-06 *
XEC.2 921 138 3.357854 -4.122734 16.245469 9.856150e-07
BA.2.12.1 107150 144 3.258876 -6.741124 21.482248 7.211527e-08 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6283_T|C, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11109_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13931_A|G, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21697_C|T, 21711_C|T, 21718_G|A, 21738_T|C,
21765_21770, 21777_G|A, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23285_G|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23905_T|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28419_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29320_A|G, 29510_A|C, 29734_29759

Case 72 (XEC): USA/TX-USAFSAM-S23573/2025


Target: 5350 samples Number of changes: 144
BC: XEC.39 + MC.28.1.1 BC BR: 140-141 BC BR coord: 28958 - 28959
Direction L1: >> Initial region span: 1-140,141-144Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.45e-16 Rec. model vs L2: 2.01e-177
Flags: Model_2BP_Bad_L1_opp

XEC.39 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.39 155 140 243.880226 NaN NaN NaN * * *
KP.3.3 1715 144 242.728929 239.080917 -172.161835 8.229747e-03 *
XEC.18 165 140 230.499372 230.499372 -154.998744 1.545752e-06 *
XEC.19 59 140 229.962991 229.962991 -153.925982 9.052995e-07 *
XEC.29 135 140 226.268740 226.268740 -146.537480 2.249439e-08 *
XEC.15 127 140 225.086160 225.086160 -144.172320 6.877573e-09 *
XEC.36 30 140 223.100395 223.100395 -140.200790 9.448452e-10 *
XEC.8 592 143 222.587547 218.677428 -131.354857 1.131378e-11
XEC.4 192 140 222.050643 222.050643 -138.101287 3.306370e-10 *
XEC.38 34 140 222.033037 222.033037 -138.066074 3.257145e-10 *
|||||

MC.28.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.28.1.1 129 141 9.672369 NaN NaN NaN * * *
BF.30 60 142 8.072392 -1.927608 13.855216 9.166088e-06 *
BQ.2 47 142 7.991120 -2.008880 14.017760 8.461365e-06 *
BA.2.10.2 48 141 7.665913 7.665913 -5.331826 1.346603e-01 * *
JC.5 136 142 7.493066 -8.808982 27.617964 9.424059e-09 *
XBB.1.5.75 85 141 7.399568 7.399568 -4.799137 1.033122e-01 * *
JC.5.1 53 142 7.314594 -8.932458 27.864915 8.358390e-09 *
LB.1.4 235 141 7.006154 7.006154 -4.012308 6.959935e-02 * *
JN.1.32.1 55 142 6.823753 -3.176247 16.352494 2.639292e-06 *
JN.1.18.2 51 141 6.690809 6.690809 -3.381617 5.079283e-02 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6040_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 15921_G|T, 16332_C|T, 17410_C|T, 18163_A|G,
18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20946_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23383_G|A, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A,
23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26176_C|T, 26270_C|T, 26289_T|C, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C,
28884_G|C, 28958_C|A, 29272_C|T, 29510_A|C, 29734_29759, 29769_C|T

Case 72 (XEC): USA/VA-CAV_VAS3N_00022765_01/2025


Target: 5350 samples Number of changes: 140
BC: LE.1 + XEC.18 BC BR: 5-6 BC BR coord: 672 - 673
Direction L1: << Initial region span: 1-5,8-140Gap history (edge excluded): 5-8
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.87e-01
Rec. model vs L1: 4.15e-98Rec. model vs L2: 5.48e-08
Flags: Model_1BP_Best

LE.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LE.1 27 5 14.065224 NaN NaN NaN * * *
LF.7.9.3 20 3 7.111420 -1.801681 15.603363 1.288006e-07
XFB.3 56 3 6.955858 -1.957243 15.914486 1.103068e-07
NY.12.1 17 3 6.912387 -2.000714 16.001429 1.054531e-07
XEL.5 19 3 6.879637 -2.033464 16.066928 1.018260e-07
MC.13.2.4 37 3 6.742160 -10.006521 32.013041 3.519912e-11
LC.1 10 3 6.582895 -2.330207 16.660413 7.581270e-08
XEC.35.1 28 3 6.538559 -2.374542 16.749085 7.247675e-08
LF.6 27 3 6.511211 -2.401891 16.803781 7.068729e-08
LF.7.1.11 20 3 6.449363 -2.463738 16.927476 6.623876e-08
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 8 291.947526 NaN NaN NaN * * *
XEC.9 305 8 291.564307 285.175132 -280.350264 6.736800e-01 * *
XEC.31 66 8 291.162153 284.774240 -279.548480 4.515812e-01 * *
XEC.39 155 8 291.108436 284.729319 -279.458637 4.317105e-01 * *
XEC.14 193 8 285.929177 271.692770 -253.385541 9.422455e-07 *
XEC.17 13 8 284.947219 278.574574 -267.149148 9.164528e-04 * *
XEC.32 42 8 281.704123 275.331478 -260.662956 3.571285e-05 * *
MC.24.1 25 8 281.340506 274.967861 -259.935721 2.491601e-05 * *
XEC.4 192 8 280.978934 274.590540 -259.181080 1.703910e-05 * *
XEC.38 34 8 280.882119 274.509473 -259.018946 1.572907e-05 * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_G|T, 670_T|G, 897_C|A, 1250_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 17502_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T,
26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/VA-USAFSAM-S23569/2025


Target: 5350 samples Number of changes: 143
BC: KP.3.1.1 + XEC.2 BC BR: 16-17 BC BR coord: 6806 - 6807
Direction L1: << Initial region span: 1-16,17-143Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.77e-63 Rec. model vs L2: 6.45e-25
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 16 15.169287 NaN NaN NaN * * *
XEC.39 155 13 13.642950 -2.753732 41.507464 1.641615e-08
XEC.9 305 13 13.335366 -3.054843 42.109685 1.216139e-08
LB.1.3.1 292 5 6.340081 -19.620476 75.240952 7.778484e-16
BW.1.1.2 55 4 6.082585 -83.370911 202.741822 1.601850e-43
B.1.110.3 764 3 5.658809 -99.490300 234.980600 1.598802e-50
XEC.38 34 13 5.581698 -10.808511 57.617021 5.212299e-12
XEC.8.1 12 13 5.338246 -11.138974 58.277949 3.747246e-12
XEC.18.3 13 13 5.258203 -11.132006 58.264011 3.784906e-12
KP.2.2 1334 5 4.776716 -21.178024 78.356048 1.634540e-16
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 17 263.750030 NaN NaN NaN * * *
XEC.14 193 17 256.339898 256.339898 -240.679797 6.051707e-04 * *
XEC.9 305 2 255.763346 248.818189 -225.636378 3.280827e-07
XEC.18 165 4 255.329855 247.205583 -222.411165 6.525260e-08
XEC.31 66 17 254.103847 254.103847 -236.207693 6.474850e-05 * *
XEC.8 592 17 247.985337 247.985337 -223.970674 1.423467e-07 *
KP.3.3 1715 8 247.348464 241.874679 -211.749358 3.160881e-10
XEC.40 52 17 246.856476 246.856476 -221.712952 4.598273e-08 *
XEC.2.1 265 17 246.672384 246.672384 -221.344769 3.821644e-08 *
XEK.1.2 33 17 245.799046 241.412235 -210.824471 1.985461e-10 *



Target sequence

, 106_C|T, 241_C|T, 601_C|T, 670_T|G, 897_C|A, 2060_G|A, 2062_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5477_C|T, 6183_A|G, 6794_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A,
23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23191_C|T, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26155_26157, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G,
26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28085_G|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/VT-25-003495-WGS-01/2025


Target: 5350 samples Number of changes: 144
BC: XEC.33 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,16-144Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01
Rec. model vs L1: 4.89e-32Rec. model vs L2: 3.98e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 14 17.783166 NaN NaN NaN * * *
XEC.4 192 14 17.681102 17.681102 -3.362204 9.003245e-01 * *
XEC.16 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.4.3 10 12 15.079158 -7.384864 46.769728 1.171677e-11
XEC.32 42 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.17 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.22 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.18.3 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.24 11 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.25 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 267.720756 NaN NaN NaN * * *
XEC.14 193 28 241.392023 226.792602 -177.585205 3.710592e-14
XEC.29 135 16 238.681067 228.681067 -181.362133 2.443927e-13 *
XEC.30 135 28 231.322752 216.715897 -157.431793 1.555087e-18
XEC.25 13 28 229.899943 208.838593 -141.677185 5.911337e-22
XEC.2.1 265 28 226.378931 202.081034 -128.162068 6.852594e-25
XEC.5 126 28 223.567610 208.968190 -141.936379 6.731998e-22
XEC.9 305 24 222.145129 212.116921 -148.233841 1.563148e-20
XEC.8 592 28 219.655610 205.052805 -134.105610 1.342397e-23
XEC.18 165 28 219.150953 204.551533 -133.103065 8.101443e-24



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A,
28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/VT-25-003503-WGS-01/2025


Target: 5350 samples Number of changes: 143
BC: XEC.33 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,16-143Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01
Rec. model vs L1: 4.89e-32Rec. model vs L2: 3.98e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 14 17.783166 NaN NaN NaN * * *
XEC.4 192 14 17.681102 17.681102 -3.362204 9.003245e-01 * *
XEC.16 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.4.3 10 12 15.079158 -7.384864 46.769728 1.171677e-11
XEC.32 42 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.17 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.22 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.18.3 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.24 11 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.25 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 267.271358 NaN NaN NaN * * *
XEC.14 193 27 241.392023 226.343204 -176.686408 3.710592e-14
XEC.29 135 16 238.231668 228.231668 -180.463337 2.443927e-13 *
XEC.30 135 27 231.322752 216.266498 -156.532997 1.555087e-18
XEC.25 13 27 229.899943 208.389194 -140.778389 5.911337e-22
XEC.2.1 265 27 226.378931 201.639197 -127.278394 6.921464e-25
XEC.5 126 27 223.567610 208.518791 -141.037583 6.731998e-22
XEC.9 305 23 222.145129 211.667522 -147.335045 1.570984e-20
XEC.8 592 27 219.655610 204.603407 -133.206814 1.342397e-23
XEC.18 165 27 219.150953 204.102134 -132.204269 8.101443e-24



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16308_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/VT-25-003998-WGS-01/2025


Target: 5350 samples Number of changes: 143
BC: XEC.22 + XEC.2 BC BR: 12-13 BC BR coord: 6183 - 6184
Direction L1: << Initial region span: 1-12,15-143Gap history (edge excluded): 12-15
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.30e-01
Rec. model vs L1: 2.60e-51Rec. model vs L2: 1.05e-17
Flags: Model_1BP_Best

XEC.22 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.22 23 12 15.079158 NaN NaN NaN * * *
XEC.16 23 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.4.3 10 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.32 42 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.17 13 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.18.3 13 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.25 13 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.24 11 12 15.079158 15.079158 -6.158317 1.000000 * *
XEC.4.1 68 12 15.049528 15.049528 -6.099057 0.970446 * *
XEC.13 30 12 15.045257 15.045257 -6.090514 0.965605 * *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 15 267.720756 NaN NaN NaN * * *
XEC.14 193 27 241.392023 213.189659 -142.379318 3.692085e-14
XEC.29 135 15 238.681067 206.515046 -129.030091 4.659679e-17 *
XEC.30 135 27 231.322752 203.112954 -122.225907 1.555087e-18
XEC.25 13 27 229.899943 195.235649 -106.471299 5.881854e-22
XEC.2.1 265 27 226.378931 188.478091 -92.956182 6.852594e-25
XEC.5 126 27 223.567610 195.365246 -106.730493 6.698422e-22
XEC.9 305 23 222.145129 192.431162 -100.862325 3.558920e-23
XEC.8 592 27 219.655610 191.451553 -98.903105 1.335702e-23
XEC.18 165 27 219.150953 190.954669 -97.909337 8.142052e-24



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16308_C|T,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C,
22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A,
22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G,
23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T, 26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): USA/CA-LACPHL-AY11147/2025


Target: 5350 samples Number of changes: 145
BC: XEC.33 + XEC.2 BC BR: 14-15 BC BR coord: 7842 - 7843
Direction L1: << Initial region span: 1-14,16-145Gap history (edge excluded): 14-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.90e-01
Rec. model vs L1: 5.46e-32Rec. model vs L2: 3.98e-24
Flags: Model_1BP_Best

XEC.33 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.33 169 14 17.783166 NaN NaN NaN * * *
XEC.4 192 14 17.681102 17.681102 -3.362204 9.003245e-01 * *
XEC.16 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.4.3 10 12 15.079158 -7.384864 46.769728 1.171677e-11
XEC.32 42 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.17 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.22 23 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.18.3 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.24 11 12 15.079158 8.682101 14.635797 1.111089e-04 *
XEC.25 13 12 15.079158 8.682101 14.635797 1.111089e-04 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 16 271.351893 NaN NaN NaN * * *
XEC.14 193 28 245.024085 230.424664 -184.849328 3.710592e-14
XEC.29 135 16 242.299684 232.299684 -188.599368 2.419610e-13 *
XEC.25 13 28 237.617708 216.556357 -157.112714 3.513813e-20
XEC.30 135 28 234.867262 220.260406 -164.520813 1.428367e-18
XEC.2.1 265 28 229.985151 205.687253 -135.374506 6.683403e-25
XEC.5 126 28 227.124600 212.525180 -149.050360 6.245568e-22
XEC.18 165 28 226.505286 211.905866 -147.811731 3.359768e-22
XEC.9 305 24 225.734380 215.706172 -155.412344 1.501856e-20
XEC.39 155 5 223.777073 209.859526 -143.719052 4.346875e-23



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 915_A|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6638_C|T, 7842_A|G, 7852_T|C, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10273_T|C, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16308_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22594_C|T, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25613_C|T, 26060_C|T,
26093_A|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-0398E8C9-B516-48A2-86FD-3E54BF5C21F7


Target: 5350 samples Number of changes: 144
BC: KP.3.1.1 + XEC.9 BC BR: 17-18 BC BR coord: 7090 - 7091
Direction L1: << Initial region span: 1-17,18-144Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.62e-76 Rec. model vs L2: 3.24e-24
Flags: Model_2BP_Bad_L1_opp

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 17 4.454387 NaN NaN NaN * * *
BA.5.1.23 4202 4 3.636291 -62.310012 188.620023 1.010018e-29
BA.5 6418 4 3.241758 -52.349998 168.699995 2.137479e-25
BF.10 8612 4 3.031054 -75.376164 214.752327 2.139299e-35
AY.4.2.2 19573 3 3.012210 -92.753561 249.507121 6.056663e-43
BQ.1.1 36940 4 2.419308 -50.695834 165.391668 1.118560e-24
XBB.1.16.6 4784 4 2.033307 -65.997527 195.995054 2.522216e-31
BA.5.1 53705 4 1.871199 -44.187545 152.375091 7.477302e-22
BA.2 443141 4 1.075408 -39.273974 142.547949 1.019301e-19
P.1 10221 3 1.032244 -128.975452 321.950905 1.127424e-58
|||||

XEC.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.9 305 18 277.842271 NaN NaN NaN * * *
XEC.13 30 14 273.572892 262.580198 -263.160397 2.358665e-07
XEC.2 921 17 269.368766 265.772089 -269.544179 5.728826e-06 *
XEC.16 23 17 266.523748 262.913957 -263.827913 3.297273e-07 *
XEC.31 66 17 262.279959 258.670168 -255.340337 4.726882e-09 *
XEC.28 39 17 261.637429 258.027638 -254.055277 2.492449e-09 *
XEC.19 59 17 261.386508 257.776717 -253.553434 1.931440e-09 *
XEC.14 193 17 261.348784 257.738993 -253.477985 1.865009e-09 *
XEC.17 13 17 260.351159 256.741368 -251.482737 6.860984e-10 *
XEC.8 592 17 260.218741 256.608950 -251.217899 6.024599e-10 *



Target sequence

, 241_C|T, 379_C|T, 509_G|A, 670_T|G, 897_C|A, 2030_G|A, 2060_G|A, 2790_C|T, 3037_C|T, 3177_C|T, 3431_G|T, 3565_T|C, 3736_C|T, 4184_G|A, 4321_C|T, 5184_C|A, 6183_A|G, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13372_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-336E7E7C-A753-4F02-8767-9C96D4FFF043


Target: 5350 samples Number of changes: 145
BC: KP.2.3.13 + XEC.14 BC BR: 5-6 BC BR coord: 1297 - 1298
Direction L1: << Initial region span: 1-5,9-145Gap history (edge excluded): 5-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.57e-156Rec. model vs L2: 1.49e-23
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.13 25 5 11.399879 NaN NaN NaN * * *
XEC.4.3 10 4 10.581513 0.581513 8.836974 0.000020 * *
KP.3.3.10 55 4 9.569912 -0.430088 10.860176 0.000007 *
JN.1.34 83 4 8.927300 -1.072700 12.145400 0.000004 *
KS.2 18 4 8.837955 -1.162045 12.324089 0.000004 *
MC.10 221 4 8.648716 -1.351284 12.702569 0.000003 *
JN.1.40 26 4 8.488168 -1.511832 13.023663 0.000002 *
LZ.1 28 4 8.453281 -1.546719 13.093438 0.000002 *
LF.7.1 165 5 8.288343 8.288343 -6.576686 0.044601 * *
NY.7 36 4 8.201967 -1.798033 13.596067 0.000002 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 269.682855 NaN NaN NaN * * *
XEC.2 921 8 256.626219 236.626219 -173.252439 5.135572e-14 *
XEC.2.2 273 9 249.494751 219.494751 -138.989503 1.866914e-21 *
XEC.4 192 9 248.969849 235.256251 -170.512501 1.304985e-14 *
KP.3.3 1715 9 248.613194 230.342798 -160.685596 9.620984e-17 *
XEC.28 39 9 247.386239 233.672640 -167.345279 2.687943e-15 *
XEC.8 592 9 245.830690 232.105196 -164.210393 5.592137e-16 *
XEC.29 135 9 241.851981 228.138382 -156.276764 1.060719e-17 *
XEC.17 13 9 240.815307 227.101708 -154.203415 3.749159e-18 *
MC.24.1 25 9 237.862520 223.494994 -146.989989 1.019301e-19 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 1973_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11752_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13554_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-3F05C326-1A96-41EB-A33D-E8C815FBAD27


Target: 5350 samples Number of changes: 148
BC: JN.1.7.5 + XEC.2 BC BR: 16-17 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-7,18-148Gap history (edge excluded): 7-18
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.93e-121Rec. model vs L2: 2.93e-39
Flags: Model_2BP_Bad_L1_opp

JN.1.7.5 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.7.5 427 7 28.134461 NaN NaN NaN * * *
JN.2 574 5 18.992844 -17.389622 70.779244 2.307954e-16
BA.4.1 18821 6 8.227998 -18.361891 72.723781 8.749063e-17 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 18 237.681481 NaN NaN NaN * * *
XEC.8 592 20 225.436821 209.046612 -130.093225 8.070907e-09
XEC.14 193 24 223.343498 205.993885 -123.987770 3.822295e-10
XEC.9 305 24 222.826061 209.459085 -130.918170 1.222235e-08
XEC.4 192 24 217.444787 209.930296 -131.860591 1.955568e-08
XEC.33 169 9 216.080219 197.721356 -107.442712 9.739515e-14
XEC.30 135 20 213.698307 197.308098 -106.616197 6.463631e-14
XEC.31 66 24 210.925853 193.576240 -99.152479 1.543074e-15
XEK.1 88 24 210.797798 185.434540 -82.869081 4.500177e-19
XEC.29 135 24 210.500397 179.153884 -70.307768 8.430635e-22



Target sequence

, 241_C|T, 670_T|G, 688_.|CAT, 689_T|A, 692_T|A, 694_T|G, 897_C|A, 958_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4276_C|T, 4321_C|T, 5512_C|T, 6183_A|G, 6543_C|T,
7842_A|G, 8293_C|T, 8393_G|A, 9298_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18891_G|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23222_G|A,
23271_C|T, 23403_A|G, 23423_23428, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26159_26161, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27223_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
27970_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-4CC641EA-D8D1-4993-9310-51B7F11A72A7


Target: 5350 samples Number of changes: 151
BC: XEC.14 + JG.2 + XEC.14BC BR: 9-10, 14-15 BC BR coord: 3566 - 3567, 5647 - 5648
Direction L1: << Initial region span: 1-9,10-14,19-151Gap history (edge excluded): 9-19 -> 14-19
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.91e-11
Rec. model vs L1: 4.50e-21Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.14 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 1.437887 None None None * * *
|||||

JG.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JG.2 72 14 13.822197 NaN NaN NaN * * *
DN.1.1 313 13 7.057412 -2.942588 29.885177 5.236644e-08 *
XBB.1 3166 13 6.520895 5.880687 12.238625 3.562065e-04 * *
PQ.14 26 10 6.443512 -25.783951 75.567901 6.306190e-18
KP.2.25.2 16 10 6.443512 -11.409630 46.819261 1.103444e-11
XBB.1.16.1 1702 13 5.865231 -4.134769 32.269538 1.593098e-08 *
HV.1 11771 13 5.520429 5.358811 13.282378 2.117721e-04 * *
BN.2.1 21 10 5.344899 -33.085466 90.170932 4.260076e-21
XBB.1.5.68 27 10 5.344899 -12.508243 49.016485 3.673045e-12
B.1.523 109 10 5.335683 -34.834734 93.669467 7.402902e-22
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 19 223.817661 NaN NaN NaN * * *
KP.3.3 1715 19 221.579348 204.827434 -95.654869 1.949856e-03 * *
XEC.2 921 19 220.572159 197.068229 -80.136457 8.356968e-07 *
XEC.18 165 18 217.457353 210.353067 -106.706134 4.916442e-01 * *
XEC.29 135 18 210.590163 189.510638 -65.021276 4.352938e-10 *
XEC.9 305 19 210.340949 198.161717 -82.323433 2.485591e-06 *
XEC.8 592 19 210.278391 193.090424 -72.180848 1.561553e-08 *
XEC.13 30 19 206.824660 189.723059 -65.446118 5.397041e-10 *
XEC.2.2 273 25 206.133276 166.186123 -18.372247 3.227481e-20
XEC.4 192 19 205.048200 187.922193 -61.844386 8.876755e-11 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1848_C|T, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3619_C|T, 3644_G|A, 4184_G|A, 4321_C|T, 5646_C|T, 5806_C|T, 6183_A|G, 6478_T|C, 7420_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9445_T|C, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
13585_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21812_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23644_C|A, 23854_C|A, 23948_G|T, 24367_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 25603_C|A, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-5514ABAB-1EBE-40B9-AD35-BB8653DA8DC4


Target: 5350 samples Number of changes: 142
BC: XEC.2 + XEC.1 + XEC.2 BC BR: 4-5, 6-7 BC BR coord: 1153 - 1154, 2060 - 2061
Direction L1: << Initial region span: 1-4,5-6,7-142Gap history (edge excluded): 4-7 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 1.76e-05
Rec. model vs L1: 6.09e-10Rec. model vs L2: 5.45e-37
Flags: Model_2BP_Best

XEC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 4 4.922764 None None None * * *
|||||

XEC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.1 99 6 8.426421 NaN NaN NaN * * *
XEC.5 126 6 7.502265 7.502265 -5.004529 3.965314e-01 * *
XEC.30 135 6 7.403194 7.403194 -4.806389 3.605949e-01 * *
XEC.4 192 6 7.081051 7.081051 -4.162102 2.605397e-01 * *
HC.1 10 5 6.052145 -3.947855 17.895709 4.222851e-06 *
HC.2 19 5 6.052145 -13.664830 37.329660 2.549382e-10 *
B.1.558 181 5 6.052145 -3.947855 17.895709 4.222851e-06 *
B.1.385 53 5 6.052145 -14.191177 38.382354 1.508101e-10 *
BF.7.5.1 141 5 6.045028 -6.944386 23.888773 2.112972e-07 *
B.1.1.251 36 5 6.023975 -3.976025 17.952051 4.118589e-06 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 7 276.776131 NaN NaN NaN * * *
KP.3.3 1715 8 268.793520 263.786093 -227.572186 1.658114e-08 *
XEC.39 155 8 268.305693 253.011567 -206.023135 3.468098e-13 *
XEC.28 39 8 267.386239 252.026439 -204.052877 1.295124e-13 *
XEC.33 169 8 266.989165 251.678096 -203.356193 9.172330e-14 *
XEC.8 592 8 264.881989 249.531997 -199.063994 1.068431e-14 *
XEC.14 193 8 261.797265 246.489946 -192.979892 5.110828e-16 *
XEC.17 13 8 260.815307 245.534126 -191.068251 1.966709e-16 *
MC.24.1 25 8 257.862520 242.540517 -185.081034 9.840748e-18 *
XEC.15 127 8 257.700818 242.403764 -184.807527 8.598018e-18 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A,
28883_G|C, 28884_G|C, 28896_C|T, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-5D565D61-4013-4E04-BC27-A4C69F4AEB42


Target: 5350 samples Number of changes: 148
BC: XEC.14 + JG.2 + XEC.14BC BR: 8-9, 13-14 BC BR coord: 3566 - 3567, 5647 - 5648
Direction L1: << Initial region span: 1-8,9-13,17-148Gap history (edge excluded): 8-17 -> 13-17
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.25e-14
Rec. model vs L1: 4.50e-21Rec. model vs L2: 0.00e+00
Flags: Model_2BP_Best

XEC.14 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 8 11.437887 None None None * * *
|||||

JG.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JG.2 72 13 13.822197 NaN NaN NaN * * *
DN.1.1 313 12 7.057412 -2.942588 27.885177 5.236644e-08 *
XBB.1 3166 12 6.520895 5.880687 10.238625 3.562065e-04 * *
KP.2.25.2 16 9 6.443512 -11.409630 44.819261 1.103444e-11
PQ.14 26 9 6.443512 -25.783951 73.567901 6.306190e-18
XBB.1.16.1 1702 12 5.865231 -4.134769 30.269538 1.593098e-08 *
KP.3.1.1 12013 14 5.674926 2.067218 17.865564 7.849977e-06 *
HV.1 11771 12 5.520429 5.358811 11.282378 2.117721e-04 * *
BN.2.1 21 9 5.344899 -33.085466 88.170932 4.260076e-21
XBB.1.5.68 27 9 5.344899 -12.508243 47.016485 3.673045e-12
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 17 233.817661 NaN NaN NaN * * *
KP.3.3 1715 17 231.579348 225.503108 -143.006215 3.473526e-02 * *
XEC.29 135 16 220.590163 219.510638 -131.021276 8.653168e-05 * *
XEC.9 305 17 220.340949 217.110534 -126.221067 7.849977e-06 *
XEC.8 592 17 220.278391 223.090424 -138.180848 3.104198e-03 * *
XEC.2 921 17 218.963593 205.513627 -103.027254 7.231424e-11 *
XEC.2.2 273 23 216.133276 196.186123 -84.372247 6.415881e-15
XEC.4 192 17 215.048200 217.922193 -127.844386 1.764603e-05 * *
XEC.18 165 16 214.822419 227.718133 -147.436266 3.182239e-01 * *
XEC.40 52 17 214.499918 217.393383 -126.786765 1.043860e-05 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3619_C|T, 3644_G|A, 4184_G|A, 4321_C|T, 5646_C|T, 6183_A|G, 6478_T|C, 7420_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9445_T|C, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21812_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23644_C|A, 23854_C|A, 23948_G|T, 24367_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
25603_C|A, 25703_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-7035C5F5-2143-4E09-9861-E8C8C4DF8C86


Target: 5350 samples Number of changes: 146
BC: KP.2.3.13 + XEC.14 BC BR: 5-6 BC BR coord: 1297 - 1298
Direction L1: << Initial region span: 1-5,9-146Gap history (edge excluded): 5-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.57e-156Rec. model vs L2: 1.49e-23
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.13 25 5 11.399879 NaN NaN NaN * * *
XEC.4.3 10 4 10.581513 0.581513 8.836974 0.000020 * *
KP.3.3.10 55 4 9.569912 -0.430088 10.860176 0.000007 *
JN.1.34 83 4 8.927300 -1.072700 12.145400 0.000004 *
KS.2 18 4 8.837955 -1.162045 12.324089 0.000004 *
MC.10 221 4 8.648716 -1.351284 12.702569 0.000003 *
JN.1.40 26 4 8.488168 -1.511832 13.023663 0.000002 *
LZ.1 28 4 8.453281 -1.546719 13.093438 0.000002 *
LF.7.1 165 5 8.288343 8.288343 -6.576686 0.044601 * *
NY.7 36 4 8.201967 -1.798033 13.596067 0.000002 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 259.682855 NaN NaN NaN * * *
XEC.2 921 8 246.626219 226.626219 -151.252439 5.135572e-14 *
XEC.2.2 273 9 239.494751 209.494751 -116.989503 1.866914e-21 *
XEC.4 192 9 238.969849 225.256251 -148.512501 1.304985e-14 *
KP.3.3 1715 9 238.613194 220.342798 -138.685596 9.620984e-17 *
XEC.28 39 9 237.386239 223.672640 -145.345279 2.687943e-15 *
XEC.8 592 9 235.830690 222.105196 -142.210393 5.592137e-16 *
XEC.29 135 9 231.851981 218.138382 -134.276764 1.060719e-17 *
XEC.17 13 9 230.815307 217.101708 -132.203415 3.749159e-18 *
MC.24.1 25 9 227.862520 213.494994 -124.989989 1.019301e-19 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 1973_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11752_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13554_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A, 23948_G|T, 24353_A|G, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-BA12F5F9-8A6C-421B-9AED-9577268198D2


Target: 5350 samples Number of changes: 147
BC: NY.13 + XEC.2 BC BR: 6-7 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-5,10-147Gap history (edge excluded): 5-10
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.09e-149Rec. model vs L2: 1.10e-09
Flags: Model_2BP_Bad_L1_opp

NY.13 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NY.13 463 5 10.744395 NaN NaN NaN * * *
JV.2 16 3 8.889772 -34.957105 93.914210 8.555135e-18
BN.1 1200 3 7.896973 -22.103027 68.206055 3.257699e-12
XEC.6 45 8 6.741873 5.660779 12.678441 3.724751e+00 *
BA.4.2 1792 3 4.163430 -29.734487 83.468974 1.582137e-15
BF.7 11554 3 2.993263 -20.472019 64.944038 1.671023e-11
JN.1.4 8971 3 2.546824 -10.304045 44.608090 4.340961e-07
XFH.1 10 5 2.405006 -7.594994 39.189988 6.524149e-06 *
BA.4.1 18821 3 1.813614 -32.083089 88.166179 1.508871e-16
BA.5.2.1 73935 3 1.543024 -18.419704 60.839408 1.298034e-10
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 10 245.529961 NaN NaN NaN * * *
KP.3.3 1715 6 230.169448 228.439843 -154.879686 2.830180e-04 *
XEC.9 305 6 221.357549 215.071148 -128.142295 4.418724e-10
XEC.8 592 6 220.878384 214.603878 -127.207755 2.775556e-10
XEC.2.1 265 27 220.181434 202.118986 -102.237973 1.049986e-15
MC.24.1 25 15 217.769997 208.234144 -114.468289 4.752193e-13
XEC.32 42 15 215.862282 206.326429 -110.652859 7.037066e-14
XEC.33 169 15 214.739782 205.167781 -108.335561 2.217081e-14
XEC.2.2 273 10 214.497112 205.578206 -109.156412 3.340737e-14 *
XEC.39 155 15 214.238891 204.670248 -107.340496 1.344727e-14



Target sequence

, 241_C|T, 310_A|G, 670_T|G, 897_C|A, 949_A|G, 2060_G|A, 2790_C|T, 3037_C|T, 3411_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5144_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10567_T|C, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22181_C|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24023_C|T, 24378_C|T, 24424_A|T, 24469_T|A, 24784_C|T, 24863_C|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 25931_C|A, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-C9583D6A-0A9C-425E-AAB8-A1943D5F1208


Target: 5350 samples Number of changes: 140
BC: XEC.18 + XEK.1 BC BR: 129-130 BC BR coord: 28290 - 28291
Direction L1: >> Initial region span: 1-129,132-140Gap history (edge excluded): 129-132
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 2.42e-02
Rec. model vs L1: 2.87e-09Rec. model vs L2: 1.98e-54
Flags: Model_1BP_Best

XEC.18 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 129 270.753531 NaN NaN NaN * * *
XEC.4 192 129 264.623005 264.623005 -253.246010 2.176581e-03 * *
XEC.6 45 129 263.978329 263.978329 -251.956657 1.141970e-03 * *
XEC.33 169 129 261.535429 261.535429 -247.070857 9.903869e-05 * *
XEC.8 592 129 259.416998 259.416998 -242.833996 1.188777e-05 * *
XEC.24 11 129 259.075313 259.075313 -242.150626 8.461365e-06 *
XEC.36 30 129 258.291226 258.291226 -240.582452 3.859395e-06 *
XEC.17 13 129 257.101994 257.101994 -238.203988 1.174110e-06 *
XEC.15 127 129 256.804479 256.804479 -237.608957 8.741621e-07 *
XEC.2 921 129 255.308199 255.308199 -234.616398 1.960296e-07 *
|||||

XEK.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEK.1 88 132 16.314988 NaN NaN NaN * * *
XEC.4 192 132 15.867486 -4.892340 33.784679 6.408243e-01 * *
KP.3.3.4 292 132 14.421916 -6.337910 36.675820 1.503183e-01 * *
KP.3.3 1715 132 14.148719 -6.611107 37.222213 1.147499e-01 * *
KP.1.1.2 12 137 10.631340 -17.877607 59.755215 1.463031e-06
NY.1 25 137 9.810029 -18.516597 61.033194 7.753122e-07
JN.1.11.1 226 132 9.410985 -11.348840 46.697680 1.002759e-03 * *
MU.2.1 37 137 9.348718 -18.977908 61.955816 4.870008e-07
JN.1.22 516 137 9.181984 -19.257350 62.514701 3.699123e-07
KP.3 769 132 8.888332 -11.871494 47.742987 5.961609e-04 * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T,
10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17304_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T,
18894_C|T, 19716_C|T, 19891_G|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25897_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28303_28311, 28314_G|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C,
28905_C|T, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-D4306C2B-0C5B-4513-BF63-848147D0A912


Target: 5350 samples Number of changes: 146
BC: XEC.32 + KP.3.3.4 BC BR: 136-137 BC BR coord: 28361 - 28362
Direction L1: >> Initial region span: 1-136,139-146Gap history (edge excluded): 136-139
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.05e-12 Rec. model vs L2: 3.23e-71
Flags: Model_2BP_Bad_L1_opp

XEC.32 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 136 247.693106 NaN NaN NaN * * *
XEC.9 305 137 240.633597 240.169535 -190.339069 5.394287e-04 * *
XEC.4 192 143 240.615726 228.122891 -166.245783 3.168524e-09
XEC.8 592 136 237.364079 237.364079 -184.728157 3.263909e-05 * *
XEC.18 165 136 235.303136 235.303136 -180.606272 4.159981e-06 *
XEC.31 66 136 228.539778 228.539778 -167.079557 4.798320e-09 *
XEC.33 169 136 227.175551 227.175551 -164.351103 1.225398e-09 *
XEC.14 193 143 226.991046 225.558160 -161.116320 2.437203e-10
XEC.3 29 136 225.214395 225.214395 -160.428790 1.726077e-10 *
XEC.24 11 136 221.567155 221.567155 -153.134310 4.486268e-12 *
|||||

KP.3.3.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.4 292 139 14.531099 NaN NaN NaN * * *
KP.3.3 1715 139 13.328665 -6.671335 35.342671 1.645304e-05 * *
JN.1.30 57 143 12.916045 -15.429459 52.858917 2.581230e-09
JN.1.23 10 143 11.386342 -16.959161 55.918323 5.589283e-10
KP.3.1.10 51 143 10.010592 -4.002922 30.005843 2.363965e-04 *
JN.1.4.7 159 143 8.813068 -19.532435 61.064870 4.277788e-11
XEC.11.1.1 12 139 8.450744 -11.549256 45.098513 1.249940e-07 *
KP.1.1 593 143 8.437611 -9.428045 40.856089 1.041342e-06
JN.2 574 143 8.231969 0.230623 21.538754 1.632594e-02 *
XBB.1.33 27 144 8.163116 -30.182387 82.364775 1.013872e-15



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 6664_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12412_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T, 18086_C|A, 18163_A|G,
18492_A|G, 18657_C|T, 18861_A|T, 18888_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22030_G|A, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23600_T|C, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370,
28657_C|T, 28708_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29137_C|T, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-336E7E7C-A753-4F02-8767-9C96D4FFF043


Target: 5350 samples Number of changes: 145
BC: KP.2.3.13 + XEC.14 BC BR: 5-6 BC BR coord: 1297 - 1298
Direction L1: << Initial region span: 1-5,9-145Gap history (edge excluded): 5-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.57e-156Rec. model vs L2: 1.49e-23
Flags: Model_2BP_Bad_L1_opp

KP.2.3.13 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.13 25 5 11.399879 NaN NaN NaN * * *
XEC.4.3 10 4 10.581513 0.581513 8.836974 0.000020 * *
KP.3.3.10 55 4 9.569912 -0.430088 10.860176 0.000007 *
JN.1.34 83 4 8.927300 -1.072700 12.145400 0.000004 *
KS.2 18 4 8.837955 -1.162045 12.324089 0.000004 *
MC.10 221 4 8.648716 -1.351284 12.702569 0.000003 *
JN.1.40 26 4 8.488168 -1.511832 13.023663 0.000002 *
LZ.1 28 4 8.453281 -1.546719 13.093438 0.000002 *
LF.7.1 165 5 8.288343 8.288343 -6.576686 0.044601 * *
NY.7 36 4 8.201967 -1.798033 13.596067 0.000002 *
|||||

XEC.14 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.14 193 9 269.682855 NaN NaN NaN * * *
XEC.2 921 8 256.626219 236.626219 -173.252439 5.135572e-14 *
XEC.2.2 273 9 249.494751 219.494751 -138.989503 1.866914e-21 *
XEC.4 192 9 248.969849 235.256251 -170.512501 1.304985e-14 *
KP.3.3 1715 9 248.613194 230.342798 -160.685596 9.620984e-17 *
XEC.28 39 9 247.386239 233.672640 -167.345279 2.687943e-15 *
XEC.8 592 9 245.830690 232.105196 -164.210393 5.592137e-16 *
XEC.29 135 9 241.851981 228.138382 -156.276764 1.060719e-17 *
XEC.17 13 9 240.815307 227.101708 -154.203415 3.749159e-18 *
MC.24.1 25 9 237.862520 223.494994 -146.989989 1.019301e-19 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1150_C|T, 1288_C|T, 1973_C|T, 2060_G|A, 2650_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10156_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11752_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13554_C|T, 14408_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20544_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23609_C|T, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 72 (XEC): IGS-10285-CVDP-F81870C3-13A3-4CE6-8567-7BF50276D37D


Target: 5350 samples Number of changes: 146
BC: XEC.39 + XEC.2 BC BR: 12-13 BC BR coord: 4387 - 4388
Direction L1: << Initial region span: 1-8,13-146Gap history (edge excluded): 8-13
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.32e-01
Rec. model vs L1: 3.76e-31Rec. model vs L2: 3.57e-24
Flags: Model_1BP_Best

XEC.39 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.39 155 8 18.622173 NaN NaN NaN * * *
XEC.3 29 7 15.661018 1.434276 21.131448 0.000002 *
XEC.22 23 7 15.661018 1.469367 21.061265 0.000002 *
XEC.29 135 7 15.661018 1.447007 21.105987 0.000002 *
XEC.32 42 7 15.661018 1.469367 21.061265 0.000002 *
XEC.36 30 7 15.661018 1.435466 21.129068 0.000002 *
XEC.24 11 7 15.661018 1.469367 21.061265 0.000002 *
XEC.4.1.4 23 7 15.661018 1.469367 21.061265 0.000002 *
XEC.4.3 10 7 15.661018 1.469367 21.061265 0.000002 *
XEC.4.7 13 7 15.661018 1.207003 21.585994 0.000002 *
|||||

XEC.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.2 921 13 231.720443 NaN NaN NaN * * *
XEC.9 305 1 215.469140 200.609909 -115.219817 3.083889e-14
XEC.2.1 265 39 210.621889 193.991464 -101.982929 4.112152e-17
XEC.8 592 10 208.733786 202.964998 -119.929996 3.249841e-13
XEC.14 193 10 208.133859 202.341176 -118.682351 1.739515e-13
XEC.33 169 39 202.459161 187.760543 -89.521085 8.098686e-20
XEC.39 155 1 200.249560 185.851827 -85.703654 1.199257e-20
XEC.31 66 39 199.956377 193.039581 -100.079161 1.590338e-17
XEC.40 52 39 199.465110 186.222970 -86.445940 1.744908e-20
XEC.29 135 39 198.105556 177.176990 -68.353981 2.048366e-24



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3511_C|T, 3535_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9220_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12525_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14206_C|T, 14408_C|T, 15714_C|T, 15756_T|A,
16293_C|T, 16326_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19545_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T,
26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26801_C|T, 26833_C|T, 26858_C|T, 26957_T|A, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28065_28119, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 78 (XFC): OZ288079


Target: 72 samples Number of changes: 143
BC: XFC.1 + JN.1.9 + XFC.1BC BR: 123-124, 140-141 BC BR coord: 26872 - 26873, 29498 - 29499
Direction L1: >> Initial region span: 1-123,124-138,141-143Gap history (edge excluded): 123-141 -> 138-141
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 8.19e-03
Rec. model vs L1: 3.78e-25Rec. model vs L2: 4.97e-148
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 123 226.595979 NaN NaN NaN * * *
LP.8.1 1124 133 180.106630 168.259560 -40.519120 4.116353e-29
XFC.1.1.1 21 111 173.892135 179.881954 -63.763909 4.581572e-24
LP.8.1.1 2345 133 167.966380 157.231562 -18.463125 6.671823e-34
NY.7 36 111 153.828652 144.876281 6.247438 2.874327e-39
NY.15 216 111 135.213296 128.662254 38.675493 2.608862e-46
NY.12 62 111 128.271821 119.529942 56.940116 2.827109e-50
NY.9 107 133 127.448928 116.332387 63.335226 1.152392e-51
PR.2 20 111 126.547589 117.862869 60.274263 5.348626e-51
NY.6 30 111 124.698817 115.813838 64.372325 6.885549e-52
|||||

JN.1.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 138 21.191121 NaN NaN NaN * * *
KP.2.1 47 133 17.010073 -8.393355 56.786711 1.041697e-10
JN.1 17255 140 16.555710 16.555710 6.888579 7.134913e+00 *
KP.2.3 4440 138 15.797610 -4.202390 48.404780 6.912047e-09 *
JN.1.4 8971 138 15.601325 -4.398675 48.797350 5.659105e-09 *
KP.3.2.3 759 133 15.452380 -10.046251 60.092501 2.000578e-11
MC.30 104 133 15.421587 -10.084658 60.169316 1.922134e-11
LP.8.1.4 191 133 14.888470 -10.573660 61.147320 1.177550e-11
KP.3.3.1 211 132 14.633121 -20.508222 81.016445 5.705106e-16
XEC.30 135 132 14.125068 -20.985133 81.970266 3.547920e-16
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 141 7.024671 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1683_T|C, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21595_C|T, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G,
22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A,
23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T,
24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25227_C|T, 25584_C|T, 25695_T|C, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A,
26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A,
29146_A|T, 29494_G|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): OZ288142


Target: 72 samples Number of changes: 141
BC: XFC.1 + JN.1.9 + XFC.1BC BR: 122-123, 138-139 BC BR coord: 26872 - 26873, 29498 - 29499
Direction L1: >> Initial region span: 1-122,123-138,139-141Gap history (edge excluded): 122-139 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.61e-03
Rec. model vs L1: 3.78e-25Rec. model vs L2: 2.11e-135
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 122 236.595979 NaN NaN NaN * * *
LP.8.1.1 2345 132 183.270866 172.536049 -51.072098 1.343312e-31
LP.8.1 1124 132 182.941714 171.094644 -48.189287 3.182678e-32
XFC.1.1.1 21 122 182.754099 189.881954 -85.763909 4.581572e-24 *
NY.7 36 122 162.662445 154.876281 -15.752562 2.874327e-39 *
NY.15 216 127 143.731958 138.662254 16.675493 2.608862e-46
NY.9 107 132 137.448928 126.332387 41.335226 1.152392e-51
NY.12 62 122 137.329094 129.529942 34.940116 2.827109e-50 *
PR.2 20 122 135.572072 127.862869 38.274263 5.348626e-51 *
NY.6 30 122 133.560781 125.813838 42.372325 6.885549e-52 *
|||||

JN.1.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 138 24.592399 NaN NaN NaN * * *
KP.2.1 47 132 17.010073 1.606645 34.786711 1.041697e-10
JN.1 17255 138 16.519214 16.519214 4.961572 3.127833e-04 * *
KP.2.3 4440 137 15.797610 5.797610 26.404780 6.912047e-09 *
JN.1.4 8971 137 15.601325 5.601325 26.797350 5.659105e-09 *
KP.3.2.3 759 132 15.452380 -0.046251 38.092501 2.000578e-11
MC.30 104 132 15.421587 -0.084658 38.169316 1.922134e-11
LP.8.1.4 191 132 14.888470 -0.573660 39.147320 1.177550e-11
KP.3.3.1 211 131 14.633121 -10.508222 59.016445 5.705106e-16
XEC.30 135 131 14.125068 -10.985133 59.970266 3.547920e-16
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 139 7.024671 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1683_T|C, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11650_C|T, 11727_G|A, 11902_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C,
22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T,
22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A,
23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T,
24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T,
26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29494_G|A,
29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY11434/2025


Target: 72 samples Number of changes: 148
BC: LP.8.1 + XFC.1 BC BR: 6-7 BC BR coord: 1956 - 1957
Direction L1: << Initial region span: 1-6,8-148Gap history (edge excluded): 6-8
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 9.62e-40 Rec. model vs L2: 4.69e-12
Flags: Model_2BP_Bad_L1_opp

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 6 13.756682 NaN NaN NaN * * *
JN.1.47 202 4 11.496264 -8.503736 33.007471 2.150824e-10
JN.1.7.1 120 4 10.442759 -9.557241 35.114482 7.526544e-11
JN.1.14 45 4 10.017007 -9.982993 35.965986 4.896086e-11
LB.1.3.2 390 5 9.838643 -0.161357 16.322714 9.052995e-07 *
KP.2.3 4440 4 5.440081 4.213069 7.573863 7.191685e-05 *
BQ.1.1.57 173 3 5.088486 -28.363835 72.727671 5.099369e-19
KP.3.1.1 12013 4 4.452614 1.591607 12.816785 5.209639e-06
BA.5.1.21 324 3 4.442390 -15.017612 46.035225 3.185490e-13
BA.4.1.5 35 3 3.521913 -26.478087 68.956174 3.358625e-18
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 8 307.914399 NaN NaN NaN * * *
XFC.1.1.1 21 8 285.600524 275.600524 -241.201048 2.035723e-10 *
LP.8.1 1124 1 256.731388 242.974706 -175.949412 1.379943e-24
NY.7 36 8 245.458851 235.458851 -160.917702 7.518620e-28 *
LP.8.1.1 2345 8 231.968814 221.968814 -133.937628 1.041131e-33 *
PF.2 56 10 213.675881 199.317445 -88.634890 1.508565e-43
NY.7.1 28 8 212.868359 202.868359 -95.736718 5.278141e-42 *
NY.15 216 8 210.634010 200.634010 -91.268021 5.647195e-43 *
PR.2 20 6 209.786515 203.281867 -96.563733 7.953196e-42
JN.1.16.1 466 8 204.128479 202.080282 -94.160564 2.395457e-42 *



Target sequence

, 241_C|T, 670_T|G, 694_T|A, 897_C|A, 1426_C|T, 1954_G|A, 2110_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY11873/2025


Target: 72 samples Number of changes: 151
BC: XFC.1 + JN.1.9 BC BR: 132-133 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-132,133-151Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02
Rec. model vs L1: 1.50e-16Rec. model vs L2: 3.09e-140
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 132 250.752171 NaN NaN NaN * * *
LP.8.1 1124 143 239.082446 226.566437 -163.132874 3.137530e-11
XFC.1.1.1 21 132 227.087220 227.087220 -164.174440 5.277413e-11 *
NY.7 36 132 204.682589 204.682589 -119.365177 9.867899e-21 *
LP.8.1.1 2345 143 194.716254 182.970924 -75.941848 3.660328e-30
NY.15 216 137 177.743799 171.060354 -52.120708 2.460780e-35
NY.12 62 132 171.805098 171.805098 -53.610196 5.183488e-35 *
NY.7.1 28 132 171.016159 171.016159 -52.032318 2.352499e-35 *
PF.2 56 132 167.980703 167.980703 -45.961405 1.130956e-36 *
NY.3 209 132 166.385269 166.385269 -42.770539 2.294806e-37 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 133 23.325594 NaN NaN NaN * * *
JN.1.4 8971 133 16.560932 16.560932 4.878136 1.153447e-03 * *
JN.1 17255 133 16.052407 16.052407 5.895186 6.926401e-04 * *
JN.1.18.6 29 134 15.159394 5.159394 27.681211 1.291340e-08 *
MC.2 396 134 12.659426 2.659426 32.681148 1.059997e-09 *
MC.25 26 139 12.601213 -1.983858 41.967715 1.018607e-11
XFC.1 51 145 12.287468 -5.763569 49.527138 2.324735e-13
LB.1.2.2 175 134 11.479504 1.479504 35.040992 3.257145e-10 *
NW.1 111 139 11.314438 -3.270632 44.541265 2.817982e-12
KP.2.3 4440 134 10.600542 9.539073 18.921855 1.030981e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9360_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY11904/2025


Target: 72 samples Number of changes: 152
BC: XFC.1 + JN.1.9 BC BR: 133-134 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-133,134-152Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02
Rec. model vs L1: 1.49e-16Rec. model vs L2: 5.56e-147
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 133 254.881633 NaN NaN NaN * * *
LP.8.1 1124 144 242.650511 230.134503 -170.269005 1.792186e-11
XFC.1.1.1 21 133 232.103985 232.103985 -174.207971 1.285118e-10 *
NY.7 36 133 207.214447 207.214447 -124.428895 1.992294e-21 *
LP.8.1.1 2345 144 198.522629 186.777300 -83.554599 2.644687e-30
PP.1 127 133 175.774250 175.774250 -61.548500 4.417077e-35 *
NY.7.1 28 133 173.799332 173.799332 -57.598665 6.129195e-36 *
PF.2 56 133 171.169341 171.169341 -52.338682 4.417829e-37 *
NY.3 209 133 170.559510 170.559510 -51.119020 2.400431e-37 *
NY.15 216 138 169.625723 162.942278 -35.884557 1.177512e-40
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 134 23.325594 NaN NaN NaN * * *
JN.1.4 8971 134 16.560932 16.560932 4.878136 1.153447e-03 * *
JN.1 17255 134 16.052407 16.052407 5.895186 6.926401e-04 * *
JN.1.18.6 29 135 15.159394 5.159394 27.681211 1.291340e-08 *
MC.2 396 135 12.659426 2.659426 32.681148 1.059997e-09 *
MC.25 26 140 12.601213 -1.983858 41.967715 1.018607e-11
XFC.1 51 146 12.287468 -5.763569 49.527138 2.324735e-13
LB.1.2.2 175 135 11.479504 1.479504 35.040992 3.257145e-10 *
NW.1 111 140 11.314438 -3.270632 44.541265 2.817982e-12
KP.2.3 4440 135 10.600542 9.539073 18.921855 1.030981e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13381_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T,
24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C,
27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12024/2025


Target: 72 samples Number of changes: 151
BC: XFC.1 + JN.1.9 BC BR: 132-133 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-132,133-151Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02
Rec. model vs L1: 1.49e-16Rec. model vs L2: 1.11e-146
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 132 264.881633 NaN NaN NaN * * *
XFC.1.1.1 21 132 242.103985 242.103985 -196.207971 1.285118e-10 *
LP.8.1 1124 143 229.483631 216.967622 -145.935245 1.559378e-21
NY.7 36 132 217.214447 217.214447 -146.428895 1.992294e-21 *
LP.8.1.1 2345 143 208.522629 196.777300 -105.554599 2.644687e-30
NY.7.1 28 132 183.799332 183.799332 -79.598665 6.129195e-36 *
PF.2 56 132 181.169341 181.169341 -74.338682 4.417829e-37 *
NY.15 216 137 179.625723 172.942278 -57.884557 1.177512e-40
LP.8.1.6 76 132 174.290113 174.290113 -60.580226 4.542165e-40 *
PR.2 20 132 173.010444 173.010444 -58.020888 1.262891e-40 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 133 23.325594 NaN NaN NaN * * *
JN.1.4 8971 133 16.560932 16.560932 4.878136 1.153447e-03 * *
JN.1 17255 133 16.052407 16.052407 5.895186 6.926401e-04 * *
JN.1.18.6 29 134 15.159394 5.159394 27.681211 1.291340e-08 *
MC.2 396 134 12.659426 2.659426 32.681148 1.059997e-09 *
MC.25 26 139 12.601213 -1.983858 41.967715 1.018607e-11
XFC.1 51 145 12.287468 -5.763569 49.527138 2.324735e-13
LB.1.2.2 175 134 11.479504 1.479504 35.040992 3.257145e-10 *
NW.1 111 139 11.314438 -3.270632 44.541265 2.817982e-12
KP.2.3 4440 134 10.600542 9.539073 18.921855 1.030981e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12565_G|T, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17427_G|A, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25487_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12139/2025


Target: 72 samples Number of changes: 151
BC: NY.3 + XFC.1 BC BR: 17-18 BC BR coord: 6743 - 6744
Direction L1: << Initial region span: 1-14,18-151Gap history (edge excluded): 14-18
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.50e-09
Rec. model vs L1: 6.67e-86Rec. model vs L2: 9.60e-22
Flags: Model_1BP_Best

NY.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NY.3 209 14 39.222924 NaN NaN NaN * * *
NY.9 107 14 30.172358 0.172358 35.655285 1.565861e-11 *
NY.7 36 14 27.114003 -2.885997 41.771995 7.378764e-13 *
PD.2 21 14 27.114003 -2.885997 41.771995 7.378764e-13 *
LP.8.1.14 51 14 27.074397 -2.925603 41.851205 7.089439e-13 *
NY.3.1 24 14 27.071443 -2.928557 41.857114 7.054080e-13 *
PP.2 22 14 27.067483 -2.932517 41.865035 7.018898e-13 *
NY.16.1 20 14 27.062709 -2.937291 41.874581 7.018898e-13 *
PF.1 19 14 27.059935 -2.940065 41.880129 6.983891e-13 *
LP.8.1.11 75 14 27.046705 -2.953295 41.906590 6.879914e-13 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 18 256.902897 NaN NaN NaN * * *
XFC.1.1.1 21 18 240.907031 240.907031 -195.814062 1.125352e-07 *
LP.8.1 1124 18 237.256975 237.256975 -188.513949 2.924916e-09 *
LP.8.1.1 2345 1 190.222440 181.975222 -77.950443 2.872860e-33
NY.7 36 18 187.141818 187.141818 -88.283636 5.028581e-31 *
NY.15 216 18 161.864834 161.864834 -37.729668 5.304598e-42 *
NY.3 209 1 161.759841 136.711223 12.577555 6.309207e-53
NY.9 107 2 156.772363 146.800473 -7.600946 1.520569e-48
PF.2 56 18 155.801181 155.801181 -25.602363 1.232130e-44 *
NY.7.1 28 18 154.300011 154.300011 -22.600022 2.749253e-45 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3885_C|T, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 6742_G|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20759_C|T, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21786_G|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12211/2025


Target: 72 samples Number of changes: 148
BC: XFC.1 + JN.1.9 BC BR: 129-130 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-129,130-148Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02
Rec. model vs L1: 1.50e-16Rec. model vs L2: 4.36e-152
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 129 280.752171 NaN NaN NaN * * *
XFC.1.1.1 21 129 257.087220 257.087220 -234.174440 5.277413e-11 *
LP.8.1 1124 140 245.915566 233.399557 -186.799114 2.729960e-21
NY.7 36 129 234.682589 234.682589 -189.365177 9.867899e-21 *
LP.8.1.1 2345 140 224.716254 212.970924 -145.941848 3.660328e-30
NY.7.1 28 129 201.016159 201.016159 -122.032318 2.352499e-35 *
PF.2 56 129 197.980703 197.980703 -115.961405 1.130956e-36 *
NY.15 216 134 195.359263 188.675819 -97.351637 1.028811e-40
PP.1 127 129 191.414854 191.414854 -102.829708 1.593318e-39 *
LP.8.1.6 76 129 191.406857 191.406857 -102.813713 1.577464e-39 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 130 23.325594 NaN NaN NaN * * *
JN.1.4 8971 130 16.560932 16.560932 4.878136 1.153447e-03 * *
JN.1 17255 130 16.052407 16.052407 5.895186 6.926401e-04 * *
JN.1.18.6 29 131 15.159394 5.159394 27.681211 1.291340e-08 *
MC.2 396 131 12.659426 2.659426 32.681148 1.059997e-09 *
MC.25 26 136 12.601213 -1.983858 41.967715 1.018607e-11
XFC.1 51 142 12.287468 -5.763569 49.527138 2.324735e-13
LB.1.2.2 175 131 11.479504 1.479504 35.040992 3.257145e-10 *
NW.1 111 136 11.314438 -3.270632 44.541265 2.817982e-12
KP.2.3 4440 131 10.600542 9.539073 18.921855 1.030981e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7093_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12402/2025


Target: 72 samples Number of changes: 154
BC: XFC.1 + JN.1.9 BC BR: 135-136 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-135,136-154Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.28e-02
Rec. model vs L1: 1.50e-16Rec. model vs L2: 3.04e-152
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 135 257.836990 NaN NaN NaN * * *
LP.8.1 1124 146 222.952890 210.436882 -128.873763 2.596818e-21
XFC.1.1.1 21 135 219.890700 219.890700 -147.781400 3.316621e-17 *
LP.8.1.1 2345 146 212.278179 200.532850 -109.065699 1.302945e-25
NY.7 36 135 211.010518 211.010518 -130.021037 4.614885e-21 *
NY.7.1 28 135 177.779578 177.779578 -63.559157 1.708265e-35 *
PF.2 56 135 175.216726 175.216726 -58.433453 1.313983e-36 *
NY.15 216 140 172.644387 165.960942 -39.921884 1.256593e-40
LP.8.1.6 76 135 167.978050 167.978050 -43.956100 9.472603e-40 *
PP.1 127 135 167.503055 167.503055 -43.006111 5.890870e-40 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 136 23.325594 NaN NaN NaN * * *
JN.1.4 8971 136 16.560932 16.560932 4.878136 1.153447e-03 * *
JN.1 17255 136 16.052407 16.052407 5.895186 6.926401e-04 * *
JN.1.18.6 29 137 15.159394 5.159394 27.681211 1.291340e-08 *
MC.2 396 137 12.659426 2.659426 32.681148 1.059997e-09 *
MC.25 26 142 12.601213 -1.983858 41.967715 1.018607e-11
XFC.1 51 148 12.287468 -5.763569 49.527138 2.324735e-13
LB.1.2.2 175 137 11.479504 1.479504 35.040992 3.257145e-10 *
NW.1 111 142 11.314438 -3.270632 44.541265 2.817982e-12
KP.2.3 4440 137 10.600542 9.539073 18.921855 1.030981e-06 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1148_G|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T,
7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11200_C|T, 11288_11296, 11727_G|A, 12493_C|T, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 25997_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T,
27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T,
29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12567/2025


Target: 72 samples Number of changes: 155
BC: XFC.1 + JN.1.7 + XFC.1BC BR: 134-135, 152-153 BC BR coord: 26872 - 26873, 29509 - 29510
Direction L1: >> Initial region span: 1-134,136-152,153-155Gap history (edge excluded): 134-153 -> 134-136
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.56e-02
Rec. model vs L1: 2.68e-23Rec. model vs L2: 7.82e-130
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 134 243.755002 NaN NaN NaN * * *
LP.8.1 1124 146 219.764580 207.490506 -116.981013 1.582675e-19
XFC.1.1.1 21 134 219.367917 226.495772 -154.991544 2.838955e-11 *
LP.8.1.1 2345 142 216.986475 207.776614 -117.553227 2.104582e-19
NY.7 36 134 197.435890 189.649726 -81.299451 2.828644e-27 *
LP.8.1.4 191 142 170.525280 149.406347 -0.812693 9.405825e-45
NY.7.1 28 134 164.513251 156.621727 -15.243453 1.278885e-41 *
PF.2 56 134 160.985318 153.069696 -8.139392 3.673552e-43 *
NY.15 216 139 158.567301 153.497596 -8.995192 5.647195e-43
PP.1 127 134 154.603936 146.847255 4.305491 7.271149e-46 *
|||||

JN.1.7 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.7 1974 136 19.702918 NaN NaN NaN * * *
JN.1 17255 135 13.585285 13.585285 14.829430 4.842422e+01 * *
LP.8.1.6 76 148 8.749941 -19.153460 80.306919 2.925912e-13
KP.3.1.1 12013 136 8.046951 7.781907 26.436187 1.458758e-01 * *
JN.1.4 8971 135 7.369652 7.369652 27.260695 9.681048e-02 * *
KP.2.3 4440 136 7.361657 6.300188 29.399625 3.320682e-02 * *
MC.25 26 144 5.827046 -14.380015 70.760030 3.467507e-11
KQ.1 383 141 5.623898 -8.966401 59.932802 7.793311e-09
BA.2.56 900 152 5.434323 -22.843164 87.686328 7.306588e-15
FL.17 35 152 4.955677 -59.223042 160.446084 1.158994e-30
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 153 7.024671 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 888_C|T, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3231_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7217_T|C,
7842_A|G, 8293_C|T, 8393_G|A, 8525_G|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T,
12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17733_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G,
24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C,
27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 27879_C|T, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29020_A|G, 29510_A|C,
29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY12730/2025


Target: 72 samples Number of changes: 150
BC: XFC.1 + JN.1.9 BC BR: 130-131 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-130,131-150Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.15e-07
Rec. model vs L1: 8.89e-23Rec. model vs L2: 2.22e-152
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 130 282.179410 NaN NaN NaN * * *
XFC.1.1.1 21 130 257.610003 257.610003 -233.220007 2.134935e-11 *
LP.8.1 1124 141 247.027765 234.511757 -187.023513 1.982358e-21
NY.7 36 130 235.764988 235.764988 -189.529975 6.953791e-21 *
LP.8.1.1 2345 141 226.152937 214.407607 -146.815215 3.697115e-30
NY.7.1 28 130 201.944408 201.944408 -121.888815 1.426863e-35 *
PF.2 56 130 199.468567 199.468567 -116.937134 1.200890e-36 *
NY.15 216 135 196.789969 190.106524 -98.213049 1.028811e-40
LP.8.1.6 76 130 192.435188 192.435188 -102.870377 1.057406e-39 *
PP.1 127 130 192.389265 192.389265 -102.778529 1.010877e-39 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 131 23.660979 NaN NaN NaN * * *
JN.1.4 8971 131 17.171097 17.171097 11.657806 1.518549e-03 * *
JN.1 17255 131 16.760803 16.760803 12.478394 1.007785e-03 * *
MC.25 26 137 15.341461 0.756391 44.487218 1.128457e-10
KB.1 86 147 12.770066 -37.806556 121.613113 2.023437e-27
XDD.1 18 147 12.743619 -37.890161 121.780323 1.858552e-27
KB.2 24 147 12.738800 -37.971354 121.942707 1.715659e-27
EG.5.1.7 91 147 12.718438 -37.938227 121.876454 1.767909e-27
XDK.1 127 143 12.695712 -5.360527 56.721055 2.493298e-13
MC.2 396 132 12.676357 2.676357 40.647286 7.697156e-10 *



Target sequence

, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7093_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759, 29762_C|T

Case 78 (XFC): USA/CA-LACPHL-AY13055/2025


Target: 72 samples Number of changes: 157
BC: LP.8.1.1 + XFC.1 BC BR: 20-21 BC BR coord: 6694 - 6695
Direction L1: << Initial region span: 1-18,21-157Gap history (edge excluded): 18-21
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.86e-43 Rec. model vs L2: 7.06e-27
Flags: Model_2BP_Bad_L1_opp

LP.8.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1.1 2345 18 19.397030 NaN NaN NaN * * *
NY.1 25 18 12.872101 -7.127899 62.255799 1.907285e-08 *
MC.9.1 15 5 11.845534 -64.450330 176.900660 2.435880e-33
KP.3.2.1 70 5 10.542015 -62.988183 173.976366 1.048880e-32
XFJ.1 59 5 10.441274 -69.874613 187.749226 1.073021e-35
KP.3.3.1 211 5 9.348011 -56.616285 161.232570 6.156773e-30
MC.11 393 6 9.345400 -36.584475 121.168951 3.078021e-21
LP.8.1 1124 18 8.501551 -11.498449 70.996899 2.412952e-10 *
MC.24 831 5 8.467215 -57.510213 163.020427 2.515704e-30
NY.13 463 18 8.443691 -11.556309 71.112619 2.283823e-10 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 21 239.769652 NaN NaN NaN * * *
XFC.1.1.1 21 21 210.907031 210.907031 -125.814062 2.911319e-13 *
LP.8.1 1124 10 209.727890 203.969557 -111.939114 2.833072e-16
LP.8.1.1 2345 3 204.363168 185.153775 -74.307550 1.909883e-24
NY.7 36 10 176.142054 170.356880 -44.713759 7.135896e-31
NY.15 216 68 150.831708 143.288136 9.423727 1.256806e-42
KP.3.1 1957 20 144.723143 144.391837 7.216325 3.775655e-42 *
LP.8.1.4 191 68 144.587112 127.025122 41.949757 1.085097e-49
PF.2 56 12 144.359085 139.673023 16.653954 3.382936e-44
NY.6 30 68 142.922302 131.807138 32.385724 1.292398e-47



Target sequence

, 44_C|T, 174_G|C, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2066_A|G, 2644_C|T, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A,
6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 10729_A|G, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T,
12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 14955_A|G, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22005_A|C, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A,
24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26305_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T,
27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C,
29625_C|T, 29734_29759

Case 78 (XFC): USA/CA-LACPHL-AY13072/2025


Target: 72 samples Number of changes: 151
BC: XFC.1 + JN.1.9 BC BR: 131-132 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-131,132-151Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.56e-01
Rec. model vs L1: 1.78e-22Rec. model vs L2: 1.47e-145
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 131 260.752171 NaN NaN NaN * * *
LP.8.1 1124 143 244.675505 232.322274 -178.644547 4.497880e-13
XFC.1.1.1 21 131 237.087220 237.087220 -188.174440 5.277413e-11 *
LP.8.1.1 2345 143 222.245284 212.091270 -138.182540 7.365980e-22
NY.7 36 131 214.682589 214.682589 -143.365177 9.867899e-21 *
NY.7.1 28 131 181.016159 181.016159 -76.032318 2.352499e-35 *
LP.8.1.4 191 143 178.008479 161.478630 -36.957261 7.719458e-44
PF.2 56 131 177.980703 177.980703 -69.961405 1.130956e-36 *
NY.15 216 136 175.359263 168.675819 -51.351637 1.028811e-40
PP.1 127 131 171.414854 171.414854 -56.829708 1.593318e-39 *
|||||

JN.1.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.9 576 132 23.138211 NaN NaN NaN * * *
JN.1.4 8971 132 14.726517 14.726517 16.546966 2.215195e-04 * *
JN.1 17255 132 14.544716 14.544716 16.910568 1.850286e-04 * *
XFC.1 51 145 12.287468 -15.763569 77.527138 1.269911e-17
KP.2.3 4440 133 10.450298 9.388829 27.222341 1.067704e-06 *
KP.1.1.1 578 132 9.369149 9.369149 27.261702 1.046562e-06 *
JN.1.18.6 29 145 8.988265 -4.840606 55.681211 7.054080e-13
XDD.1.1 29 145 8.953173 -43.277945 132.555891 1.426135e-29
LE.1 27 145 8.890020 -19.131163 84.262326 4.389067e-19
JN.1.39.3 31 145 8.889973 -19.013427 84.026855 4.923978e-19



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3259_G|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 16726_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24734_C|T, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C,
27807_C|T, 27810_T|C, 27881_C|T, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/IVY-G25Z05G8/2025


Target: 72 samples Number of changes: 146
BC: XFC.1 + MC.25 + XFC.1 BC BR: 132-133, 139-140 BC BR coord: 27387 - 27388, 28880 - 28881
Direction L1: >> Initial region span: 1-132,134-139,140-146Gap history (edge excluded): 132-140 -> 132-134
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01
Rec. model vs L1: 4.85e-09Rec. model vs L2: 1.36e-215
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 132 284.875629 NaN NaN NaN * * *
XFC.1.1.1 21 132 260.282175 272.672827 -241.345654 2.312747e-11 *
LP.8.1 1124 138 245.437741 243.118748 -182.237496 3.377184e-24
NY.7 36 132 238.350148 235.826781 -167.653562 2.292854e-27 *
LP.8.1.1 2345 138 213.022632 211.772332 -119.544663 8.192618e-38
NY.7.1 28 132 205.427510 202.798782 -101.597564 1.041840e-41 *
PF.2 56 132 201.935614 199.282788 -94.565576 3.099246e-43 *
PP.1 127 132 195.518195 193.024310 -82.048620 5.923422e-46 *
LP.8.1.6 76 132 195.512826 193.045739 -82.091478 6.043083e-46 *
NY.15 216 132 192.807395 199.683932 -95.367864 4.623532e-43 *
|||||

MC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.25 26 134 14.942259 NaN NaN NaN * * *
NW.1 111 134 13.769894 3.769894 8.460211 0.310367 * *
JN.1.47.2 60 134 11.507160 1.507160 12.985680 0.032225 * *
JN.1.18.4 64 134 10.735366 0.735366 14.529267 0.014921 * *
GW.1 11 136 10.468938 -8.767402 33.534804 0.000001
MC.2 396 133 9.723046 9.723046 -3.446092 119.701363 * *
JN.1.9 576 133 9.638327 9.638327 -3.276654 109.947172 * *
LB.1.2 199 134 9.602673 -0.397327 16.794654 0.004820 * *
KQ.1 383 134 8.926897 -1.073103 18.146206 0.002442 * *
JN.1.8.1 1498 133 8.846168 2.917321 10.165359 0.131994 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 140 12.287468 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21983_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T,
23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26115_A|G,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T,
28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MA-MASPHL-14198/2025


Target: 72 samples Number of changes: 148
BC: JN.1.16.1 + XFC.1 BC BR: 13-14 BC BR coord: 4809 - 4810
Direction L1: << Initial region span: 1-13,16-148Gap history (edge excluded): 13-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.12e-04
Rec. model vs L1: 9.33e-65Rec. model vs L2: 3.02e-23
Flags: Model_1BP_Best

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 13 24.093307 NaN NaN NaN * * *
JN.1.16 332 12 23.686312 13.686312 0.627376 3.012967e-05 * *
JN.1 17255 12 18.420777 18.229291 -8.458583 2.837023e-03 * *
XEC.30 135 12 18.413069 8.413069 11.173862 1.549753e-07 *
KP.1.1.3 979 15 16.112732 8.429205 11.141590 1.573175e-07
XDY.6 11 13 13.873495 13.873495 0.253010 3.643430e-05 * *
MC.1 932 15 13.492808 10.433837 7.132326 1.168254e-06
XDY.5 17 13 12.640378 12.640378 2.719244 1.059636e-05 * *
JN.1.28 51 13 12.510761 12.510761 2.978479 9.304615e-06 *
KP.2.3.11 56 13 12.136337 12.136337 3.727325 6.394962e-06 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 16 292.619810 NaN NaN NaN * * *
XFC.1.1.1 21 16 277.511247 265.928095 -227.856189 1.888629e-10 *
LP.8.1 1124 7 252.608827 242.690934 -181.381868 1.524554e-20
LP.8.1.1 2345 7 222.698112 211.916205 -119.832410 6.572493e-34
NY.7 36 16 221.261127 216.963714 -129.927428 1.025457e-31 *
PF.2 56 16 201.018142 196.720729 -89.441458 1.654343e-40 *
JN.1.16.1 466 1 197.521316 173.428008 -42.856017 1.270302e-50
NY.15 216 7 195.669971 182.152816 -60.305632 7.818552e-47
NY.9 107 7 190.349048 178.773337 -53.546674 2.662018e-48
LF.7 58 22 189.359284 143.224339 17.551322 9.683718e-64



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13728_T|C, 14408_C|T, 15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C,
21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C,
22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MA-MASPHL-14204/2025


Target: 72 samples Number of changes: 146
BC: XFC.1 + NY.9 + XFC.1 BC BR: 11-12, 13-14 BC BR coord: 4581 - 4582, 6182 - 6183
Direction L1: << Initial region span: 1-11,12-13,14-146Gap history (edge excluded): 11-14 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 6.21e-06
Rec. model vs L1: 4.10e-16Rec. model vs L2: 7.41e-96
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 11 6.256999 None None None * * *
|||||

NY.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
NY.9 107 12 9.901323 NaN NaN NaN * * *
PP.1 127 12 8.631353 8.631353 -11.262706 2.808316e-01 * *
KP.1.1.3 979 12 7.683526 7.683526 -9.367053 1.091535e-01 * *
B.1.1.232 220 13 7.642016 -2.357984 10.715968 4.737505e-06 *
LP.8.1 1124 12 6.447326 6.447326 -6.894652 3.158730e-02 * *
MC.1.4 125 12 5.764823 5.764823 -5.529645 1.600267e-02 * *
LP.8.1.1 2345 12 5.714219 5.714219 -5.428438 1.522221e-02 * *
FL.32.1 13 13 5.208004 -9.242033 24.484065 4.870837e-09 *
NP.1 16 13 5.000364 -4.999636 15.999271 3.380743e-07 *
JN.1.7.3 19 13 4.828514 -5.171486 16.342972 2.852214e-07 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 14 297.332378 NaN NaN NaN * * *
XFC.1.1.1 21 14 278.094463 272.515666 -235.031333 3.193736e-14 *
LP.8.1 1124 5 252.615939 240.847899 -171.695797 5.654109e-28
LP.8.1.1 2345 5 222.727067 211.686359 -113.372718 1.219455e-40
NY.7 36 14 221.844343 216.314337 -122.628673 1.250112e-38 *
PF.2 56 14 201.868421 196.209946 -82.419892 2.319843e-47 *
NY.15 216 5 195.665339 194.653577 -79.307154 4.899261e-48
NY.9 107 5 190.219291 175.018008 -40.036015 1.454650e-56
NY.7.1 28 14 189.326586 183.760212 -57.520424 9.088500e-53 *
JN.1.16.1 466 14 185.066418 187.560672 -65.121345 4.062667e-51 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 13728_T|C, 14408_C|T,
15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MA-MASPHL-14213/2025


Target: 72 samples Number of changes: 148
BC: JN.1.16.1 + XFC.1 BC BR: 13-14 BC BR coord: 4809 - 4810
Direction L1: << Initial region span: 1-13,16-148Gap history (edge excluded): 13-16
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.12e-04
Rec. model vs L1: 2.29e-69Rec. model vs L2: 3.02e-23
Flags: Model_1BP_Best

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 13 24.093307 NaN NaN NaN * * *
JN.1.16 332 12 23.686312 13.686312 0.627376 3.012967e-05 * *
JN.1 17255 12 18.420777 18.229291 -8.458583 2.837023e-03 * *
XEC.30 135 12 18.413069 8.413069 11.173862 1.549753e-07 *
KP.1.1.3 979 15 16.112732 8.429205 11.141590 1.573175e-07
XDY.6 11 13 13.873495 13.873495 0.253010 3.643430e-05 * *
MC.1 932 15 13.492808 10.433837 7.132326 1.168254e-06
XDY.5 17 13 12.640378 12.640378 2.719244 1.059636e-05 * *
JN.1.28 51 13 12.510761 12.510761 2.978479 9.304615e-06 *
KP.2.3.11 56 13 12.136337 12.136337 3.727325 6.394962e-06 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 16 296.521338 NaN NaN NaN * * *
XFC.1.1.1 21 16 280.525472 268.942319 -247.884639 7.717080e-11 *
LP.8.1 1124 7 257.068190 247.150297 -204.300593 2.655683e-20
LP.8.1.1 2345 7 226.921874 216.139967 -142.279933 9.051162e-34
NY.7 36 16 226.760258 222.462845 -154.925690 5.053787e-31 *
PF.2 56 16 205.860494 201.563081 -113.126162 4.235086e-40 *
NY.15 216 7 199.434502 185.917346 -81.834693 6.763222e-47
NY.9 107 7 195.820098 184.244387 -78.488774 1.273157e-47
NY.7.1 28 16 193.918452 189.621039 -89.242077 2.749253e-45 *
JN.1.16.1 466 1 192.243379 168.150072 -46.300144 1.302903e-54



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1393_A|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4579_T|A, 4999_C|T, 5979_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
13728_T|C, 14408_C|T, 15714_C|T, 15720_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-46633/2025


Target: 72 samples Number of changes: 147
BC: XEC.28 + XFC.1 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-147Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.64e-198Rec. model vs L2: 2.95e-08
Flags: Model_2BP_Bad_L1_opp

XEC.28 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.28 39 4 9.397373 NaN NaN NaN * * *
KP.1.1.2 12 4 8.575206 8.575206 -9.150412 0.440432 * *
JN.1.39.1 40 4 8.469846 8.469846 -8.939691 0.396531 * *
LF.7.1 165 5 8.237031 5.923623 -3.847246 0.031117 * *
PY.2 17 4 8.226899 8.226899 -8.453799 0.310367 * *
MC.30.1 18 4 8.169741 8.169741 -8.339482 0.293758 * *
XEC.4.6 10 4 8.141342 8.141342 -8.282683 0.285076 * *
MD.1 19 4 8.115674 8.115674 -8.231348 0.278037 * *
JN.1.8.2 17 4 8.105650 8.105650 -8.211300 0.275271 * *
PG.6 23 4 7.924619 7.924619 -7.849237 0.229925 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 6 313.272614 NaN NaN NaN * * *
XFC.1.1.1 21 6 289.474465 269.067637 -222.135273 1.396231e-15 *
LP.8.1 1124 1 265.075276 259.980734 -203.961467 1.574782e-19
NY.7 36 6 252.290303 242.290303 -168.580605 3.270025e-27 *
LP.8.1.1 2345 1 242.865382 238.001179 -160.002359 4.481544e-29
NY.7.1 28 6 220.192287 202.884840 -89.769680 2.518703e-44 *
NY.15 216 6 216.138195 206.138195 -96.276390 6.528381e-43 *
PF.2 56 6 215.707064 205.707064 -95.414128 4.225590e-43 *
NY.13 463 3 209.653135 205.000295 -94.000589 2.087900e-43
PR.2 20 6 206.605116 196.605116 -77.210232 4.718540e-47 *



Target sequence

, 241_C|T, 516_518, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T,
25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-46650/2025


Target: 72 samples Number of changes: 147
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141 BC BR coord: 27387 - 27388, 28880 - 28881
Direction L1: >> Initial region span: 1-133,135-140,141-147Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01
Rec. model vs L1: 4.82e-09Rec. model vs L2: 1.67e-215
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 133 299.169932 NaN NaN NaN * * *
XFC.1.1.1 21 133 274.782847 287.173498 -272.346997 2.853185e-11 *
LP.8.1 1124 139 259.918781 257.599788 -213.199577 4.083858e-24
NY.7 36 133 252.850819 250.327452 -198.654904 2.828644e-27 *
LP.8.1.1 2345 139 227.499306 226.249006 -150.498012 9.906920e-38
NY.7.1 28 133 219.928181 217.299453 -132.598906 1.285296e-41 *
PF.2 56 133 216.400248 213.747422 -125.494845 3.673552e-43 *
PP.1 127 133 210.018866 207.524981 -113.049962 7.307595e-46 *
LP.8.1.6 76 133 210.013497 207.546410 -113.092820 7.455219e-46 *
NY.15 216 133 207.298786 214.175323 -126.350645 5.647195e-43 *
|||||

MC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.25 26 135 14.942259 NaN NaN NaN * * *
NW.1 111 135 13.769894 3.769894 8.460211 0.310367 * *
JN.1.47.2 60 135 11.507160 1.507160 12.985680 0.032225 * *
JN.1.18.4 64 135 10.735366 0.735366 14.529267 0.014921 * *
GW.1 11 137 10.468938 -8.767402 33.534804 0.000001
MC.2 396 134 9.723046 9.723046 -3.446092 119.701363 * *
JN.1.9 576 134 9.638327 9.638327 -3.276654 109.947172 * *
LB.1.2 199 135 9.602673 -0.397327 16.794654 0.004820 * *
KQ.1 383 135 8.926897 -1.073103 18.146206 0.002442 * *
JN.1.8.1 1498 134 8.846168 2.917321 10.165359 0.131994 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 141 12.287468 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-46834/2025


Target: 72 samples Number of changes: 145
BC: LP.8.1 + XFC.1 BC BR: 7-8 BC BR coord: 3037 - 3038
Direction L1: << Initial region span: 1-7,9-145Gap history (edge excluded): 7-9
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 3.83e-01
Rec. model vs L1: 3.15e-39Rec. model vs L2: 2.04e-06
Flags: Model_1BP_Best

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 7 12.711222 NaN NaN NaN * * *
NY.13 463 7 12.469276 12.469276 -6.938552 7.866279e-01 * *
LP.8.1.1 2345 7 11.983068 11.983068 -5.966137 4.843246e-01 * *
XEL.4 10 4 11.039560 2.120654 13.758691 2.516642e-05 *
XEC.8 592 4 9.570849 -5.622564 29.245127 1.089458e-08
KP.2.2.1 55 4 8.749548 -0.169358 18.338716 2.548514e-06
JN.1.1.3 30 4 8.331510 -7.831918 33.663837 1.201134e-09
MC.33 31 4 8.298720 -0.620186 19.240371 1.625004e-06
XEC.29 135 4 7.520580 -7.684727 33.369454 1.388558e-09
XEC.32 42 4 7.301891 -7.903416 33.806833 1.114344e-09
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 9 325.706674 NaN NaN NaN * * *
XFC.1.1.1 21 14 302.806169 291.783361 -281.566723 4.089554e-11
LP.8.1 1124 1 274.660019 261.948797 -221.897593 4.513362e-24
NY.7 36 9 264.599199 254.599199 -207.198399 2.900252e-27 *
LP.8.1.1 2345 1 242.577555 230.594486 -159.188972 1.089423e-37
PF.2 56 9 233.491859 218.052328 -134.104657 3.881257e-43 *
NY.7.1 28 9 232.501184 222.501184 -143.002367 3.323402e-41 *
NY.15 216 9 228.494494 218.494494 -134.988988 6.056663e-43 *
NY.13 463 1 219.657701 207.188425 -112.376849 7.456488e-48
PR.2 20 9 219.019373 209.019373 -116.038746 4.648290e-47 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3218_3220, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-46650/2025


Target: 72 samples Number of changes: 147
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141 BC BR coord: 27387 - 27388, 28880 - 28881
Direction L1: >> Initial region span: 1-133,135-140,141-147Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01
Rec. model vs L1: 4.82e-09Rec. model vs L2: 1.67e-215
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 133 299.169932 NaN NaN NaN * * *
XFC.1.1.1 21 133 274.782847 287.173498 -272.346997 2.853185e-11 *
LP.8.1 1124 139 259.918781 257.599788 -213.199577 4.083858e-24
NY.7 36 133 252.850819 250.327452 -198.654904 2.828644e-27 *
LP.8.1.1 2345 139 227.499306 226.249006 -150.498012 9.906920e-38
NY.7.1 28 133 219.928181 217.299453 -132.598906 1.285296e-41 *
PF.2 56 133 216.400248 213.747422 -125.494845 3.673552e-43 *
PP.1 127 133 210.018866 207.524981 -113.049962 7.307595e-46 *
LP.8.1.6 76 133 210.013497 207.546410 -113.092820 7.455219e-46 *
NY.15 216 133 207.298786 214.175323 -126.350645 5.647195e-43 *
|||||

MC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.25 26 135 14.942259 NaN NaN NaN * * *
NW.1 111 135 13.769894 3.769894 8.460211 0.310367 * *
JN.1.47.2 60 135 11.507160 1.507160 12.985680 0.032225 * *
JN.1.18.4 64 135 10.735366 0.735366 14.529267 0.014921 * *
GW.1 11 137 10.468938 -8.767402 33.534804 0.000001
MC.2 396 134 9.723046 9.723046 -3.446092 119.701363 * *
JN.1.9 576 134 9.638327 9.638327 -3.276654 109.947172 * *
LB.1.2 199 135 9.602673 -0.397327 16.794654 0.004820 * *
KQ.1 383 135 8.926897 -1.073103 18.146206 0.002442 * *
JN.1.8.1 1498 134 8.846168 2.917321 10.165359 0.131994 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 141 12.287468 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-46650/2025


Target: 72 samples Number of changes: 147
BC: XFC.1 + MC.25 + XFC.1 BC BR: 133-134, 140-141 BC BR coord: 27387 - 27388, 28880 - 28881
Direction L1: >> Initial region span: 1-133,135-140,141-147Gap history (edge excluded): 133-141 -> 133-135
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01
Rec. model vs L1: 4.82e-09Rec. model vs L2: 1.67e-215
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 133 299.169932 NaN NaN NaN * * *
XFC.1.1.1 21 133 274.782847 287.173498 -272.346997 2.853185e-11 *
LP.8.1 1124 139 259.918781 257.599788 -213.199577 4.083858e-24
NY.7 36 133 252.850819 250.327452 -198.654904 2.828644e-27 *
LP.8.1.1 2345 139 227.499306 226.249006 -150.498012 9.906920e-38
NY.7.1 28 133 219.928181 217.299453 -132.598906 1.285296e-41 *
PF.2 56 133 216.400248 213.747422 -125.494845 3.673552e-43 *
PP.1 127 133 210.018866 207.524981 -113.049962 7.307595e-46 *
LP.8.1.6 76 133 210.013497 207.546410 -113.092820 7.455219e-46 *
NY.15 216 133 207.298786 214.175323 -126.350645 5.647195e-43 *
|||||

MC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.25 26 135 14.942259 NaN NaN NaN * * *
NW.1 111 135 13.769894 3.769894 8.460211 0.310367 * *
JN.1.47.2 60 135 11.507160 1.507160 12.985680 0.032225 * *
JN.1.18.4 64 135 10.735366 0.735366 14.529267 0.014921 * *
GW.1 11 137 10.468938 -8.767402 33.534804 0.000001
MC.2 396 134 9.723046 9.723046 -3.446092 119.701363 * *
JN.1.9 576 134 9.638327 9.638327 -3.276654 109.947172 * *
LB.1.2 199 135 9.602673 -0.397327 16.794654 0.004820 * *
KQ.1 383 135 8.926897 -1.073103 18.146206 0.002442 * *
JN.1.8.1 1498 134 8.846168 2.917321 10.165359 0.131994 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 141 12.287468 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-47236/2025


Target: 72 samples Number of changes: 150
BC: LP.8.1 + XFC.1 BC BR: 13-14 BC BR coord: 4809 - 4810
Direction L1: << Initial region span: 1-12,14-150Gap history (edge excluded): 12-14
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.40e-01
Rec. model vs L1: 1.97e-30Rec. model vs L2: 9.11e-21
Flags: Model_1BP_Best

LP.8.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LP.8.1 1124 12 21.462790 NaN NaN NaN * * *
KP.2.3 4440 13 20.034250 20.034250 -10.068499 5.271130e+03 * *
LP.8.1.4 191 12 14.197412 4.197412 21.605175 6.961120e-04 * *
LP.8.1.3 77 12 13.807079 3.807079 22.385841 4.713074e-04 * *
JN.1 17255 13 12.815379 12.815379 4.369242 3.857426e+00 * *
KP.3.1.1 12013 13 12.582727 12.582727 4.834546 3.064854e+00 * *
NW.1.2 34 10 12.439477 -14.132002 58.264005 7.660070e-12
NY.13 463 12 11.826208 1.826208 26.347584 6.507305e-05 * *
LP.8.1.1 2345 12 11.339445 1.339445 27.321110 4.006530e-05 * *
XEL.4 10 4 11.039560 -8.601653 47.203306 1.931440e-09
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 14 262.472712 NaN NaN NaN * * *
XFC.1.1.1 21 15 240.052125 238.468972 -166.937945 3.756306e-11 *
LP.8.1 1124 1 239.151328 227.688538 -145.377076 7.817474e-16
LP.8.1.1 2345 6 200.395816 193.389195 -76.778390 9.925805e-31
NY.7 36 6 199.536259 192.462103 -74.924205 3.916263e-31
JN.1.16.1 466 15 194.890507 184.890507 -59.781015 2.019587e-34 *
LF.7 58 21 168.564990 132.430045 45.139911 3.327929e-57
NY.7.1 28 6 167.438243 160.364087 -10.728174 4.510144e-45
NY.6 30 6 164.087870 157.013714 -4.027428 1.582355e-46
NY.16 136 6 163.570184 156.540696 -3.081393 9.840430e-47



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1426_C|T, 1884_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4483_T|C, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T,
8393_G|A, 8937_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12704_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A,
13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T,
25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 28079_G|T, 28271_A|T, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29212_G|T, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/MN-MDH-47239/2025


Target: 72 samples Number of changes: 148
BC: XFC.1 + MC.25 + XFC.1 BC BR: 134-135, 141-142 BC BR coord: 27387 - 27388, 28880 - 28881
Direction L1: >> Initial region span: 1-134,136-141,142-148Gap history (edge excluded): 134-142 -> 134-136
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 5.04e-01
Rec. model vs L1: 4.82e-09Rec. model vs L2: 1.67e-215
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 134 289.169932 NaN NaN NaN * * *
XFC.1.1.1 21 134 264.782847 277.173498 -250.346997 2.853185e-11 *
LP.8.1 1124 140 249.918781 247.599788 -191.199577 4.083858e-24
NY.7 36 134 242.850819 240.327452 -176.654904 2.828644e-27 *
LP.8.1.1 2345 140 217.499306 216.249006 -128.498012 9.906920e-38
NY.7.1 28 134 209.928181 207.299453 -110.598906 1.285296e-41 *
PF.2 56 134 206.400248 203.747422 -103.494845 3.673552e-43 *
PP.1 127 134 200.018866 197.524981 -91.049962 7.307595e-46 *
LP.8.1.6 76 134 200.013497 197.546410 -91.092820 7.455219e-46 *
NY.15 216 134 197.298786 204.175323 -104.350645 5.647195e-43 *
|||||

MC.25 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.25 26 136 14.942259 NaN NaN NaN * * *
NW.1 111 136 13.769894 3.769894 8.460211 0.310367 * *
JN.1.47.2 60 136 11.507160 1.507160 12.985680 0.032225 * *
JN.1.18.4 64 136 10.735366 0.735366 14.529267 0.014921 * *
GW.1 11 138 10.468938 -8.767402 33.534804 0.000001
MC.2 396 135 9.723046 9.723046 -3.446092 119.701363 * *
JN.1.9 576 135 9.638327 9.638327 -3.276654 109.947172 * *
LB.1.2 199 136 9.602673 -0.397327 16.794654 0.004820 * *
KQ.1 383 136 8.926897 -1.073103 18.146206 0.002442 * *
JN.1.8.1 1498 135 8.846168 2.917321 10.165359 0.131994 * *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 142 12.287468 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6324_A|G, 6647_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26115_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/NJ-CDC-LC1136665/2025


Target: 72 samples Number of changes: 149
BC: XFC.1 + MC.2 + XFC.1 BC BR: 134-135, 145-146 BC BR coord: 27387 - 27388, 28958 - 28959
Direction L1: >> Initial region span: 1-134,135-145,147-149Gap history (edge excluded): 134-147 -> 145-147
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 3.23e-01
Rec. model vs L1: 1.57e-12Rec. model vs L2: 3.88e-171
Flags: Model_2BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 134 289.169932 NaN NaN NaN * * *
XFC.1.1.1 21 134 264.782847 261.910701 -225.821403 2.838955e-11 *
LP.8.1 1124 140 261.624109 254.402257 -210.804514 1.554558e-14
NY.7 36 134 242.850819 225.064655 -152.129310 2.828644e-27 *
LP.8.1.1 2345 140 227.683641 220.795089 -143.590179 3.954949e-29
NY.7.1 28 134 209.928181 192.036656 -86.073312 1.278885e-41 *
PF.2 56 134 206.400248 188.484626 -78.969251 3.673552e-43 *
PP.1 127 134 200.018866 182.262184 -66.524368 7.271149e-46 *
LP.8.1.6 76 134 200.013497 182.283613 -66.567227 7.455219e-46 *
NY.15 216 134 197.298786 188.912526 -79.825052 5.647195e-43 *
|||||

MC.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.2 396 145 14.983314 NaN NaN NaN * * *
JN.1.9 576 145 14.899386 14.899386 -5.798773 0.918512 * *
JN.1.7 1974 145 13.013784 13.013784 -2.027567 0.139457 * *
KP.2.3 4440 145 12.963798 12.963798 -1.927596 0.132655 * *
PY.1 82 138 11.879550 4.692712 14.614576 0.000034 *
JN.1 17255 145 11.321642 11.321642 1.356716 0.025604 * *
MC.35 258 140 10.969312 6.232109 11.535782 0.000158 *
JN.1.4 8971 145 10.901092 10.901092 2.197816 0.016823 * *
NC.1.2.2 14 140 10.791292 6.054088 11.891823 0.000132 *
LZ.5 14 140 10.791292 6.054088 11.891823 0.000132 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 147 7.024671 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
16877_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19290_C|T, 19955_C|T, 20055_A|G, 20438_G|A, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G,
22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G,
22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A,
23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T,
25584_C|T, 25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/NY-PRL-250415_82H03/2025


Target: 72 samples Number of changes: 149
BC: JN.4 + XFC.1 BC BR: 4-5 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-4,6-149Gap history (edge excluded): 4-6
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.79e-211Rec. model vs L2: 1.28e-07
Flags: Model_2BP_Bad_L1_opp

JN.4 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.4 91 4 10.251882 NaN NaN NaN * * *
JN.1.19 438 4 7.261974 7.261974 -6.523948 5.028744e-02 * *
XBF.7.1 13 3 7.184143 -2.815857 13.631714 2.118081e-06 *
KP.2.2 1334 4 6.120417 6.120417 -4.240834 1.608288e-02 * *
BF.7.19 413 3 5.920445 -4.079555 16.159109 5.978057e-07 *
LB.1.7 1971 4 5.758423 5.758423 -3.516847 1.122064e-02 * *
JN.1 17255 4 4.682442 4.682442 -1.364885 3.810480e-03 * *
BA.5.1.15 339 3 4.610322 -5.389678 18.779355 1.613000e-07 *
BM.1.1.3 341 3 4.604475 -5.395525 18.791050 1.604955e-07 *
BQ.1.1.2 1102 3 4.350924 -5.649076 19.298152 1.243706e-07 *
|||||

XFC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 6 280.269783 NaN NaN NaN * * *
XFC.1.1.1 21 18 260.907031 236.786940 -155.573880 2.868463e-15
LP.8.1 1124 6 246.405456 236.405456 -154.810912 1.961631e-15 *
LP.8.1.1 2345 6 225.548928 215.548928 -113.097856 1.719515e-24 *
NY.7 36 6 219.537001 209.537001 -101.074003 4.198795e-27 *
NY.15 216 6 194.198673 184.198673 -50.397345 4.171324e-38 *
NY.7.1 28 6 186.695195 169.387748 -20.775495 1.543024e-44 *
PF.2 56 6 182.702448 172.702448 -27.404896 4.225590e-43 *
NY.9 107 6 179.176877 169.176877 -20.353754 1.244513e-44 *
LP.8.1.4 191 6 177.046346 167.046346 -16.092692 1.478945e-45 *



Target sequence

, 241_C|T, 670_T|G, 674_G|A, 897_C|A, 1825_C|T, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G,
8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T,
22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T,
25925_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29734_29759

Case 78 (XFC): USA/NY-PRL-250512_81H01/2025


Target: 72 samples Number of changes: 149
BC: XFC.1 + JN.1 BC BR: 129-130 BC BR coord: 26872 - 26873
Direction L1: >> Initial region span: 1-129,130-149Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 4.63e-03
Rec. model vs L1: 1.93e-18Rec. model vs L2: 1.21e-83
Flags: Model_1BP_Best

XFC.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XFC.1 51 129 280.752171 NaN NaN NaN * * *
XFC.1.1.1 21 129 257.087220 257.087220 -234.174440 5.277413e-11 *
LP.8.1 1124 140 245.915566 233.399557 -186.799114 2.729960e-21
NY.7 36 129 234.682589 234.682589 -189.365177 9.867899e-21 *
LP.8.1.1 2345 140 224.716254 212.970924 -145.941848 3.660328e-30
NY.7.1 28 129 201.016159 201.016159 -122.032318 2.352499e-35 *
PF.2 56 129 197.980703 197.980703 -115.961405 1.130956e-36 *
NY.15 216 134 195.359263 188.675819 -97.351637 1.028811e-40
PP.1 127 129 191.414854 191.414854 -102.829708 1.593318e-39 *
LP.8.1.6 76 129 191.406857 191.406857 -102.813713 1.577464e-39 *
|||||

JN.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1 17255 130 14.340323 NaN NaN NaN * * *
JN.1.9 576 130 13.325594 13.325594 19.348812 3.624024e-01 * *
KP.3.1.1 12013 131 7.560725 7.295681 31.408638 8.717569e-04 * *
EG.5.1.13 511 146 7.353268 -43.249112 132.498224 9.749465e-26
LP.8.1.1 2345 131 6.572054 6.148954 33.702093 2.774139e-04 * *
JN.1.4 8971 130 6.560932 6.560932 32.878136 4.180122e-04 * *
JG.3 1482 146 6.256479 -44.399894 134.799787 3.087039e-26
LP.1 659 136 6.138066 -8.508009 63.016017 1.192260e-10
BA.2.86.1 1343 142 5.562791 -16.218628 78.437256 5.345159e-14
EG.5.1.1 4177 146 5.218272 -17.978801 81.957601 9.196072e-15



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 1954_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4999_C|T, 6183_A|G, 6255_C|T, 6647_G|A, 6694_G|A, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18303_C|T, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|G, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23598_A|G, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24819_A|G, 24872_G|T, 24990_C|T, 25000_C|T, 25207_C|T, 25584_C|T, 25925_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27247_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27484_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28311_C|T, 28362_28370, 28519_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29625_C|T, 29711_G|T, 29734_29759

Case 81 (XFM): USA/CT-DPH-1298970001/2025


Target: 4 samples Number of changes: 151
BC: LF.7.9 + MC.1 BC BR: 141-142 BC BR coord: 28271 - 28272
Direction L1: >> Initial region span: 1-141,142-151Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.03e-19 Rec. model vs L2: 1.82e-208
Flags: Model_2BP_Bad_L1_opp

LF.7.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.9 20 141 335.593566 NaN NaN NaN * * *
LF.7.6.2 17 121 238.279720 221.159594 -116.319188 2.002216e-50
XFJ.1 59 141 196.032277 196.032277 -66.064553 2.441691e-61 *
XFJ.3 14 141 190.874228 190.874228 -55.748457 1.408973e-63 *
LF.7 58 121 151.037108 134.065403 57.869194 2.996630e-88
LF.7.9.1 48 121 143.116416 117.572463 90.855075 2.055633e-95
LF.7.2.1 67 121 138.660760 121.667790 82.664420 1.240375e-93
LF.7.1 165 123 136.267638 128.473831 69.052338 1.119249e-90
PY.1 82 121 135.288811 102.949113 120.101774 9.195180e-102
PC.3.1 27 121 134.590562 117.470436 91.059127 1.860014e-95
|||||

MC.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.1 932 142 7.683264 NaN NaN NaN * * *
JN.1.7.5 427 145 7.201075 -1.269791 28.539582 1.290901e-04 *
LB.1.3 778 145 6.549281 -1.947511 29.895022 6.539923e-05 *
KP.2.3 4440 142 6.376026 6.376026 13.247948 2.698201e-01 * *
GV.1 137 149 6.069949 -10.751732 47.503464 9.857828e-09
NY.3 209 145 5.453218 -3.037381 32.074762 2.209852e-05 *
KS.1 505 145 5.312971 -3.257166 32.514332 1.773448e-05 *
XEC.4 192 148 5.041013 -12.123325 50.246651 2.492449e-09
JN.1.39 1007 145 4.953672 -3.570287 33.140575 1.294242e-05 *
JN.1.4 8971 142 4.697798 4.697798 16.604405 5.053950e-02 * *



Target sequence

, 241_C|T, 569_G|A, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4504_G|A, 4579_T|A, 5239_C|T, 6070_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8338_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15207_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A,
21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21928_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22884_T|G,
22895_G|C, 22896_T|C, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T,
25000_C|T, 25207_C|T, 25413_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26555_A|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28660_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29711

Case 81 (XFM): USA/NY-PRL-250422_82C10/2025


Target: 4 samples Number of changes: 152
BC: LF.7.9 + JN.1.2 BC BR: 141-142 BC BR coord: 28271 - 28272
Direction L1: >> Initial region span: 1-141,142-152Gap history (edge excluded):
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 2.93e-20 Rec. model vs L2: 1.08e-155
Flags: Model_2BP_Bad_L1_opp

LF.7.9 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.9 20 141 335.997567 NaN NaN NaN * * *
LF.7.6.2 17 120 235.094567 225.422215 -106.844430 9.456190e-49
XFJ.1 59 141 201.101587 201.101587 -58.203174 2.592235e-59 *
XFJ.3 14 141 196.713834 196.713834 -49.427667 3.230674e-61 *
LF.7 58 120 147.547708 137.726937 68.546126 7.767148e-87
LF.7.1 165 137 145.523314 140.666455 62.667090 1.469222e-85
LF.7.9.3 20 120 144.070262 127.448147 89.103707 2.678464e-91
LF.7.9.1 48 120 139.552185 121.413898 101.172203 6.410894e-94
LF.7.2.1 67 120 135.262966 125.463460 93.073081 3.679690e-92
XFG.3 480 81 133.717473 113.857393 116.285215 3.339276e-97
|||||

JN.1.2 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.2 650 142 10.289153 NaN NaN NaN * * *
JN.1.7.5 427 145 9.488295 1.017429 19.965142 9.373865e-05 *
MC.13 807 142 9.173604 9.173604 3.652792 3.279153e-01 * *
LB.1.3 778 145 8.754250 0.257458 21.485083 4.383842e-05 *
KP.3.1.1 12013 142 8.470598 8.470598 5.058804 1.620258e-01 * *
BA.2.86.1 1343 142 8.370252 8.370252 5.259496 1.466070e-01 * *
GV.1 137 149 8.196587 -8.625094 39.250188 6.099860e-09
MC.1 932 142 8.017999 8.017999 5.964002 1.033122e-01 * *
JN.1.1 3081 142 7.872476 7.872476 6.255047 8.892162e-02 * *
NY.3 209 145 7.737843 -0.752756 23.505512 1.596678e-05 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4504_G|A, 4579_T|A, 5239_C|T, 6070_C|T, 6183_A|G, 7842_A|G, 7869_C|T, 7926_C|T, 8293_C|T, 8338_T|C,
8393_G|A, 8818_C|T, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 12892_G|A, 13339_T|C,
14408_C|T, 15207_T|C, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C,
21711_C|T, 21765_21770, 21928_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22884_T|G, 22895_G|C, 22896_T|C,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22930_T|A, 22942_T|A, 22986_C|T, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23933_A|G, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24990_C|T, 25000_C|T, 25207_C|T,
25413_C|T, 25584_C|T, 25844_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26555_A|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27414_G|A, 27807_C|T, 27810_T|C, 28271_A|T, 28311_C|T, 28362_28370, 28382_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28958_C|A, 29510_A|C, 29700_A|G, 29711, 29734_29759

Case 90 (XFA): USA/CA-LACPHL-AY11366/2025


Target: 2 samples Number of changes: 152
BC: MC.1.1 + XEC.4.1.4 BC BR: 33-34 BC BR coord: 13341 - 13342
Direction L1: << Initial region span: 1-33,38-152Gap history (edge excluded): 33-38
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 1.99e-02
Rec. model vs L1: 1.86e-143Rec. model vs L2: 1.09e-67
Flags: Model_1BP_Best

MC.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.1.1 107 33 69.885223 NaN NaN NaN * * *
KP.3.1.1 12013 34 68.900630 68.897784 -71.795568 3.734392e-01 * *
MC.24 831 30 67.572119 51.158381 -36.316761 7.376253e-09
KP.2.3 4440 36 56.378437 51.699799 -37.399597 1.265770e-08
MC.10.1 650 31 55.781856 49.360047 -32.720095 1.219286e-09
MC.1.2 49 33 55.396785 55.396785 -44.793571 5.094164e-07 *
MC.5 19 30 55.118385 37.553171 -9.106341 9.104569e-15
MC.11.3 19 30 55.118385 38.651783 -11.303566 2.721522e-14
MC.11.1 26 30 55.118385 38.705850 -11.411700 2.875399e-14
MC.23 64 30 55.086888 38.674353 -11.348707 2.790418e-14
|||||

XEC.4.1.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1.4 23 38 211.890620 NaN NaN NaN * * *
XEC.4.1 68 38 211.515947 206.194585 -158.389170 6.872893e-01 * *
XEC.4.1.1 12 38 209.689515 204.368153 -154.736307 1.108032e-01 * *
KP.3.1.1 12013 1 209.009269 140.111485 -26.222969 1.370215e-29
PT.1 10 38 204.583917 193.257299 -132.514598 1.649563e-06 *
KP.3.3 1715 8 188.685496 151.324369 -48.648738 1.017188e-24
XEC.4 192 8 179.701736 164.260081 -74.520162 4.216970e-19
JN.1 17255 1 179.339972 134.971869 -15.943738 8.026295e-32
XEC.8 592 8 174.889014 160.884994 -67.769988 1.442968e-20
KP.3.1 1957 8 166.660686 128.072404 -2.144808 8.088783e-35



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3552_C|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13264_C|T, 13297_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16056_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21255_G|C, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T,
23403_A|G, 23423_C|T, 23525_C|T, 23584_T|C, 23598_A|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25470_A|T, 25584_C|T, 26060_C|T, 26097_A|G, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27294_C|T, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 27995_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28783_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29728_29776

Case 97 (XEV): OZ249780


Target: 57 samples Number of changes: 137
BC: XEC.18 + KP.2.3 + XEC.18BC BR: 5-6, 15-16 BC BR coord: 896 - 897, 7841 - 7842
Direction L1: << Initial region span: 1-5,7-15,16-137Gap history (edge excluded): 5-16 -> 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 7.95e-01
Rec. model vs L1: 5.34e-23 Rec. model vs L2: 1.32e-56
Flags: Model_2BP_Best

XEC.18 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 5 8.722792 None None None * * *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 7 21.112612 NaN NaN NaN * * *
JN.1 17255 7 12.510614 2.510614 18.978771 1.831876e-04 * *
KP.3.1.1 12013 6 10.499322 10.499322 3.001356 5.406409e-01 * *
MC.11.1 26 7 8.460749 -1.539251 27.078501 3.191562e-06 *
MC.10.1.5 19 7 8.460749 -1.539251 27.078501 3.191562e-06 *
KP.3.2.8 26 7 8.460749 -9.077943 42.155886 1.695989e-09 *
MC.10.1.3 10 7 8.460749 -1.539251 27.078501 3.191562e-06 *
MK.2 15 7 8.460749 -1.539251 27.078501 3.191562e-06 *
MC.36.2 24 7 8.460749 -1.539251 27.078501 3.191562e-06 *
MC.30.1 18 7 8.460749 -9.190911 42.381821 1.519325e-09 *
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 16 201.704901 NaN NaN NaN * * *
XEC.2 921 14 201.361877 205.824638 -123.649275 1.000170e-02 *
XEC.4 192 7 190.709428 197.054908 -106.109816 1.553500e-06
MC.24.1 25 7 188.234502 189.348135 -90.696269 6.999585e-10
XEC.31 66 16 188.115015 196.919675 -105.839350 1.357318e-06 *
XEC.2.2 273 23 187.745352 192.329145 -96.658291 1.378066e-08
KP.3.1.1 12013 1 187.382552 176.883230 -65.766460 2.701417e-15
KP.3.3 1715 7 184.110359 185.010026 -82.020052 9.125029e-12
XEC.30 135 16 182.307800 190.738736 -93.477472 2.810229e-09 *
XEC.14 193 16 179.232730 187.979954 -87.959909 1.778643e-10 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4699_T|G, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 9693_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 14925_C|T,
15714_C|T, 15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21711_C|T, 21738_T|C, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A,
22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C,
27798_G|T, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28378_G|T, 28770_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 97 (XEV): USA/CA-LACPHL-AY11866/2025


Target: 57 samples Number of changes: 154
BC: KP.2.3.12 + KP.3.3 BC BR: 8-9 BC BR coord: 942 - 943
Direction L1: << Initial region span: 1-8,10-154Gap history (edge excluded): 8-10
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.22e-135Rec. model vs L2: 6.04e-09
Flags: Model_2BP_Bad_L1_opp

KP.2.3.12 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3.12 62 8 6.087460 NaN NaN NaN * * *
BA.5.1.1 4637 5 4.845359 -6.819697 29.639395 0.000002
NM.1 41 7 2.729300 -7.270700 30.541400 0.000002 *
|||||

KP.3.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3 1715 10 218.905592 NaN NaN NaN * * *
XEC.8 592 10 212.712221 196.437715 -76.875430 3.859395e-06 *
KP.3.1.1 12013 4 209.167576 204.813585 -93.627171 1.673923e-02 *
XEC.2 921 10 203.289361 193.289361 -70.578722 1.653833e-07 *
XEC.32 42 10 198.943693 182.657292 -49.314584 3.978963e-12 *
XEC.18 165 10 196.243094 179.962772 -43.925543 2.700957e-13 *
XEC.2.2 273 43 193.335885 164.785999 -13.571998 6.901245e-20
JN.1 17255 10 192.908348 182.908348 -49.816695 5.134698e-12 *
KP.3.1 1957 10 188.361835 178.361835 -40.723670 5.425941e-14 *
MC.24.1 25 10 182.175940 172.175940 -28.351881 1.117799e-16 *



Target sequence

, 21_C|T, 44_C|T, 135, 241_C|T, 670_T|G, 835_C|T, 897_C|A, 942_G|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 11845_T|C, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14120_C|T,
14408_C|T, 15714_C|T, 15756_T|A, 16877_C|T, 16915_C|T, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T,
21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22113_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22227_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C, 22630_G|T, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26446_T|C, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29353_C|T, 29510_A|C, 29555_C|T, 29734_29759

Case 97 (XEV): USA/MN-MDH-46878/2025


Target: 57 samples Number of changes: 146
BC: MC.11.2 + XEC.18 BC BR: 6-7 BC BR coord: 2060 - 2061
Direction L1: << Initial region span: 1-4,9-146Gap history (edge excluded): 4-9
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.45e-127Rec. model vs L2: 1.18e-17
Flags: Model_2BP_Bad_L1_opp

MC.11.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
MC.11.2 146 4 10.588478 NaN NaN NaN * * *
MU.2.1.1 10 4 9.006580 -10.993420 33.986841 0.204948 * *
MC.17 46 4 8.866818 -11.133182 34.266365 0.178173 * *
KP.2.3.4 70 4 8.506555 -11.493445 34.986889 0.124307 * *
NH.4 32 4 8.248894 -11.751106 35.502212 0.096328 * *
KP.2.6.1 49 4 8.110491 -11.889509 35.779017 0.083743 * *
LF.7.6 15 4 7.907967 -12.092033 36.184066 0.068563 * *
PH.1 63 4 7.778126 -12.221874 36.443748 0.060205 * *
PA.1 52 4 7.664742 -12.335258 36.670516 0.053665 * *
KP.2.28 22 4 7.524975 -12.475025 36.950050 0.046654 * *
|||||

XEC.18 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.18 165 9 259.750273 NaN NaN NaN * * *
XEC.4 192 9 259.326260 239.326260 -178.652519 5.658142e-07 *
MC.24.1 25 9 256.115434 250.016360 -200.032720 2.484745e-02 * *
XEC.8 592 9 253.563192 244.992634 -189.985269 1.641057e-04 * *
XEC.32 42 9 250.165396 230.165396 -160.330792 5.950267e-11 *
XEC.9 305 9 248.050341 228.050341 -156.100683 7.178002e-12 *
KP.3.3 1715 9 245.649443 225.649443 -151.298886 6.511737e-13 *
XEC.14 193 9 244.206949 224.206949 -148.413899 1.535116e-13 *
XEK.1 88 15 241.344673 207.363280 -114.726559 7.457998e-21
XEC.31 66 17 241.260839 217.396492 -134.792983 1.692762e-16



Target sequence

, 186_C|T, 241_C|T, 670_T|G, 897_C|A, 1684_C|A, 2032_T|C, 2106_C|T, 2549_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T,
15756_T|A, 17410_C|T, 18163_A|G, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T,
21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26645_C|T, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 26879_T|G, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29604_T|C, 29734_29759

Case 97 (XEV): IGS-10285-CVDP-BE7CCBB1-AFB1-4DBD-B00A-60439A98F4F0


Target: 57 samples Number of changes: 146
BC: LF.7.7.2 + XEC.4 BC BR: 5-6 BC BR coord: 896 - 897
Direction L1: << Initial region span: 1-5,7-146Gap history (edge excluded): 5-7
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 1.46e-246Rec. model vs L2: 1.10e-13
Flags: Model_2BP_Bad_L1_opp

LF.7.7.2 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.7.2 239 5 8.442286 NaN NaN NaN * * *
JN.1.46 308 5 6.836866 6.836866 -3.673733 0.200890 * *
JN.1.8.1 1498 5 6.829969 6.829969 -3.659938 0.199888 * *
BE.1.1.1 737 4 6.627662 -3.372338 16.744677 0.000007 *
JN.1.8 352 5 6.551767 6.551767 -3.103534 0.151072 * *
MC.2 396 5 6.319967 6.319967 -2.639935 0.120032 * *
KP.3.1.1 12013 6 6.297777 4.221627 1.556747 0.014699 * *
BA.5.3.1 660 4 6.175858 -3.824142 17.648285 0.000005 *
KP.1.1.3 979 5 5.992658 5.992658 -1.985317 0.086726 * *
JN.1.42 494 5 5.871571 5.871571 -1.743141 0.076536 * *
|||||

XEC.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 7 251.070415 NaN NaN NaN * * *
XEC.18 165 16 246.224447 223.999714 -143.999429 2.070780e-05 *
KP.3.3 1715 7 245.514843 235.514843 -167.029685 2.075081e+00 * *
XEC.31 66 16 243.887029 213.736280 -123.472560 7.212755e-10
XEK.1 88 14 243.290433 209.309039 -114.618078 8.636705e-12
XEC.2 921 14 240.250424 222.851307 -141.702613 6.556852e-06
MC.24.1 25 7 236.115434 226.115434 -148.230869 1.716591e-04 * *
XEC.32 42 7 230.165396 213.878995 -123.757990 8.338230e-10 *
XEC.14 193 16 229.292147 207.064018 -110.128035 9.148649e-13
XEC.24 11 16 227.045082 204.832619 -105.665238 9.837399e-14



Target sequence

, 241_C|T, 337_C|T, 521_523, 670_T|G, 897_C|A, 1684_C|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5440_A|G, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
17410_C|T, 18163_A|G, 18457_C|T, 18492_A|G, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 20178_C|T, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21711_C|T, 21738_T|C, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23593_G|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25856_A|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A,
28311_C|T, 28362_28370, 28378_G|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29734_29759

Case 102 (XEW): USA/2025CV0191/2025


Target: 19 samples Number of changes: 146
BC: AY.36 + XEC.4 BC BR: 3-4 BC BR coord: 570 - 571
Direction L1: << Initial region span: 1-3,5-146Gap history (edge excluded): 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 0.00e+00 Rec. model vs L2: 3.86e+02
Flags: Model_2BP_Bad_L1_opp

AY.36 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
AY.36 5867 3 4.804577 NaN NaN NaN * * *
AY.14 7575 3 4.312293 4.312293 1.375413 0.609571 * *
XBB.1.5.12 581 4 3.694368 2.612646 4.774707 0.111917 * *
LP.8.1.1 2345 4 3.683419 2.613291 4.773417 0.111917 * *
BA.5.2.35 1368 4 3.391462 2.304563 5.390873 0.082085 * *
BA.4.2 1792 4 3.249850 2.162952 5.674097 0.071361 * *
KP.3.1 1957 4 3.066618 1.993612 6.012777 0.060205 * *
B.1.258 3961 3 1.969245 1.969245 6.061510 0.058719 * *
BA.5.2.20 5259 4 1.791525 0.705578 8.588845 0.016573 * *
EG.5.1.1 4177 4 1.734324 0.656322 8.687355 0.015764 * *
|||||

XEC.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4 192 5 253.940174 NaN NaN NaN * * *
XEC.8 592 5 249.765041 240.967562 -169.935124 1.560756e-02 * *
KP.3.3 1715 5 240.993675 238.469257 -164.938515 1.281146e-03 * *
XEC.2 921 5 233.434693 230.894237 -149.788474 6.573824e-07 *
KP.3.1.1 12013 5 222.724692 220.189203 -128.378406 1.474673e-11 *
MC.24.1 25 5 218.688082 216.106804 -120.213609 2.480862e-13 *
XEC.32 42 5 212.649469 203.822612 -95.645225 1.152037e-18 *
XEC.15 127 5 209.861491 201.050507 -90.101014 7.182890e-20 *
XEC.30 135 5 207.355932 198.551661 -85.103323 5.896075e-21 *
XEC.9 305 5 205.593729 196.766872 -81.533745 9.893441e-22 *



Target sequence

, 186_C|T, 241_C|T, 570_A|G, 670_T|G, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7113_C|T, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11575_C|T, 11727_G|A, 12616_C|T, 12789_C|T, 12815_C|T, 12880_C|T, 13121_A|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 17410_C|T,
18163_A|G, 18492_A|G, 18647_C|T, 18657_C|T, 18894_C|T, 19716_C|T, 19955_C|T, 20055_A|G, 21608_.|TCATGCCGCTGT, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21711_C|T, 21738_T|C,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C,
22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23277_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23595_C|T, 23599_T|G, 23604_C|G, 23638_C|T, 23854_C|A, 23948_G|T, 24376_T|C, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T,
26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27382_G|C, 27383_A|T, 27384_T|C, 27797_A|G, 27807_C|T, 27810_T|C, 28077_G|T,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C

Case 122 (XFN): OZ261586


Target: 27 samples Number of changes: 134
BC: JN.1.16.1 + KP.3.3.10 BC BR: 116-117 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-116,118-134Gap history (edge excluded): 116-118
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.61e-19 Rec. model vs L2: 1.60e-29
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 116 139.541873 NaN NaN NaN * * *
KP.3.3 1715 132 138.573741 132.335787 13.328426 7.428622e-04 *
KP.3 769 116 136.593561 136.593561 4.812877 5.260206e-02 * *
KP.2.3 4440 123 131.236252 121.004250 35.991499 8.919731e-09
KP.3.1 1957 116 128.702092 128.702092 20.595817 1.959963e-05 * *
XEC.32 42 132 128.224644 112.014310 53.971380 1.111845e-12
MC.24.1 25 125 126.665191 121.201324 35.597352 1.084025e-08
KP.3.1.1 12013 134 126.256683 122.182326 33.635347 2.888337e-08
XEC.39 155 132 122.125070 115.892137 46.215726 5.357171e-11
KP.2 1589 116 120.642020 120.642020 36.715959 6.192048e-09 *
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 118 20.410343 NaN NaN NaN * * *
XEC.2.2 273 118 17.696525 7.696525 32.606951 6.620495e-02 * *
XEC.32 42 118 17.530195 7.530195 32.939610 5.613476e-02 * *
KP.3.1.1 12013 118 14.074357 4.074357 39.851287 1.773146e-03 * *
LP.8.1 1124 118 13.890711 3.890711 40.218578 1.473669e-03 * *
JN.1.11.1 226 125 10.949753 0.471441 47.057119 4.820730e-05 *
KR.1.4 24 131 10.910774 -24.624117 97.248234 6.088255e-16
MC.8 93 131 8.361014 -20.466434 88.932868 3.900838e-14
BQ.1.1.30 19 132 7.751354 -88.464439 224.928877 1.145864e-43
XEK.2 67 118 7.581529 -2.418471 52.836942 2.679179e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 13517_C|T, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ271486


Target: 27 samples Number of changes: 135
BC: KP.2.3 + XEC.4.1 + KP.2.3BC BR: 123-124, 131-132 BC BR coord: 28271 - 28272, 28883 - 28884
Direction L1: >> Initial region span: 1-123,124-126,132-135Gap history (edge excluded): 123-132 -> 126-132
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.63e-03
Rec. model vs L1: 4.36e-09 Rec. model vs L2: 1.48e-44
Flags: Model_2BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 123 133.652410 NaN NaN NaN * * *
JN.1.16.1 466 116 128.041960 123.352610 61.294779 2.479596e-07
KP.3.3 1715 125 125.747112 114.990543 78.018914 5.774410e-11
KP.3 769 116 125.731619 120.990329 66.019342 2.329563e-08
KP.2 1589 116 120.652034 125.142993 57.714014 1.485142e-06
MC.24.1 25 125 115.041345 104.833621 98.332759 2.245159e-15
XEC.32 42 125 114.306283 103.719070 100.561861 7.362220e-16
JN.1.4 8971 116 112.685369 116.216513 75.566974 1.965705e-10
KP.3.1.1 12013 116 111.034729 115.401754 77.196492 8.700983e-11
XEC.39 155 125 110.386042 99.718248 108.563504 1.348438e-17
|||||

XEC.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1 68 126 8.142610 NaN NaN NaN * * *
KP.3.3.8 15 125 6.591671 -7.964799 39.929598 4.483978e-06 *
XEC.23 142 125 6.591671 -7.964799 39.929598 4.483978e-06 *
XEC.4.3 10 125 6.591671 -13.567013 51.134026 1.658114e-08 *
XEC.24.1 18 125 6.591671 -14.167917 52.335834 9.054536e-09 *
NP.1 16 125 6.591671 -7.964799 39.929598 4.483978e-06 *
XEK.6 23 125 6.591671 -7.964799 39.929598 4.483978e-06 *
XEC.2.3.1 19 125 6.591671 -7.964799 39.929598 4.483978e-06 *
XEP.1 13 125 6.591671 -14.409436 52.818873 7.122550e-09 *
XEK.1 88 125 6.591671 -7.918279 39.836558 4.690366e-06 *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 132 4.91084 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G,
18492_A|G, 18781_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G,
22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ276300


Target: 27 samples Number of changes: 134
BC: KP.2.3 + XEC.4.1 + KP.2.3BC BR: 122-123, 130-131 BC BR coord: 28271 - 28272, 28883 - 28884
Direction L1: >> Initial region span: 1-122,123-125,131-134Gap history (edge excluded): 122-131 -> 125-131
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.63e-03
Rec. model vs L1: 4.39e-09 Rec. model vs L2: 1.65e-44
Flags: Model_2BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 122 137.290877 NaN NaN NaN * * *
KP.3.3 1715 124 129.194732 118.438164 71.123672 4.799137e-11
KP.3 769 115 128.981091 124.239801 59.520397 1.585153e-08
JN.1.16.1 466 115 127.786931 123.097581 61.804837 5.069620e-09
KP.2 1589 115 123.826221 128.317179 51.365642 9.328700e-07
MC.24.1 25 124 118.708832 108.501108 90.997784 2.313534e-15
XEC.32 42 124 118.055414 107.468201 93.063599 8.259479e-16
JN.1.4 8971 115 116.256724 119.787868 68.424264 1.851231e-10
KP.3.1.1 12013 115 114.609095 118.976120 70.047760 8.194277e-11
XEC.39 155 124 113.987950 103.320155 101.359689 1.302059e-17
|||||

XEC.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1 68 125 8.142610 NaN NaN NaN * * *
KP.3.3.4 292 124 6.591671 -7.919257 37.838514 4.690366e-06 *
XEC.24.1 18 124 6.591671 -14.167917 50.335834 9.054536e-09 *
NP.1 16 124 6.591671 -7.964799 37.929598 4.483978e-06 *
XEC.2.3.1 19 124 6.591671 -7.964799 37.929598 4.483978e-06 *
XEK.1 88 124 6.591671 -7.918279 37.836558 4.690366e-06 *
XEC.11.1.1 12 124 6.591671 -7.964799 37.929598 4.483978e-06 *
XEK.2 67 124 6.591671 -7.903241 37.806482 4.761252e-06 *
XEP.1 13 124 6.591671 -14.409436 50.818873 7.122550e-09 *
XEK.6 23 124 6.591671 -7.964799 37.929598 4.483978e-06 *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 131 4.91084 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18781_G|A,
18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A,
22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C,
22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T,
25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ276328


Target: 27 samples Number of changes: 135
BC: KP.2.3 + XEC.4.1 + KP.2.3BC BR: 123-124, 131-132 BC BR coord: 28271 - 28272, 28883 - 28884
Direction L1: >> Initial region span: 1-123,124-126,132-135Gap history (edge excluded): 123-132 -> 126-132
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.63e-03
Rec. model vs L1: 4.36e-09 Rec. model vs L2: 1.66e-44
Flags: Model_2BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 123 133.669686 NaN NaN NaN * * *
KP.3.3 1715 125 125.611888 114.855319 78.289361 4.970080e-11
KP.3 769 116 125.434961 120.693671 66.612657 1.708611e-08
JN.1.16.1 466 116 124.192687 119.503337 68.993325 5.197958e-09
KP.2 1589 116 120.275623 124.766581 58.466838 1.000511e-06
MC.24.1 25 125 115.066811 104.859087 98.281825 2.267723e-15
XEC.32 42 125 114.413394 103.826180 100.347639 8.055552e-16
JN.1.4 8971 116 112.653194 116.184339 75.631323 1.879209e-10
KP.3.1.1 12013 116 111.026735 115.393760 77.212480 8.528692e-11
XEC.39 155 125 110.411509 99.743714 108.512571 1.361990e-17
|||||

XEC.4.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1 68 126 8.142610 NaN NaN NaN * * *
XEC.4.3 10 125 6.591671 -13.567013 53.134026 1.658114e-08 *
XEC.18.3 13 125 6.591671 -13.646512 53.293025 1.530632e-08 *
KP.3.3.8 15 125 6.591671 -7.964799 41.929598 4.483978e-06 *
XEC.23 142 125 6.591671 -7.964799 41.929598 4.483978e-06 *
XEC.24.1 18 125 6.591671 -14.167917 54.335834 9.054536e-09 *
NP.1 16 125 6.591671 -7.964799 41.929598 4.483978e-06 *
XEK.6 23 125 6.591671 -7.964799 41.929598 4.483978e-06 *
XEC.2.3.1 19 125 6.591671 -7.964799 41.929598 4.483978e-06 *
XEP.1 13 125 6.591671 -14.409436 54.818873 7.122550e-09 *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 132 4.91084 None None None * * *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3695_C|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T,
10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18781_G|A, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G,
22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T,
27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28462_C|T, 28516_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ284692


Target: 27 samples Number of changes: 152
BC: KP.2.3 + XEC.32 + KP.2.3BC BR: 140-141, 148-149 BC BR coord: 28271 - 28272, 28957 - 28958
Direction L1: >> Initial region span: 1-140,141-148,149-152Gap history (edge excluded): 140-149 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.25e-05
Rec. model vs L1: 2.34e-14 Rec. model vs L2: 1.43e-12
Flags: Model_2BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 140 156.531125 NaN NaN NaN * * *
KP.3 769 150 151.054609 145.961926 38.076148 1.892873e-07
KP.3.1.1 12013 152 147.503128 146.285899 37.428202 2.619794e-07
JN.1.16.1 466 133 143.561260 138.871909 52.256181 1.577515e-10
KP.3.3 1715 150 140.815299 128.413391 73.173219 4.543858e-15
KP.2 1589 133 140.361372 144.852331 40.295339 6.238132e-08
XEC.2 921 150 139.513966 127.153776 75.692448 1.288884e-15
LF.7 58 108 138.501975 130.720924 68.558152 4.554844e-14
XEC.32 42 150 137.785198 110.510255 108.979490 7.609954e-23
JN.1 17255 133 134.267447 138.417538 53.164925 1.005868e-10
|||||

XEC.32 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.32 42 141 18.594804 NaN NaN NaN * * *
XBB.2.6 343 142 6.614007 -3.385993 26.771986 2.845819e-10 *
XEC.21 38 145 6.222233 3.592608 12.814784 3.059023e-07
XEC.24.1 18 145 6.222233 -2.610510 25.221020 6.177113e-10
XEC.2.3.1 19 145 6.222233 3.592608 12.814784 3.059023e-07
XEC.2.6 13 145 6.222233 -3.851256 27.702511 1.787559e-10
XEC.22 23 145 6.222233 3.592608 12.814784 3.059023e-07
XEC.23 142 145 6.222233 3.592608 12.814784 3.059023e-07
XEC.24 11 145 6.222233 -2.610510 25.221020 6.177113e-10
XEC.25 13 145 6.222233 3.512565 12.974870 2.823834e-07
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 149 4.91084 None None None * * *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 4885_T|C, 6183_A|G, 7842_A|G, 7869_C|T, 8293_C|T, 8393_G|A, 9344_C|T,
9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11681_C|T, 11727_G|A, 12193_T|C, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C,
14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641,
21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A,
22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A,
22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T,
23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23580_G|C, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T,
25006_C|T, 25207_C|T, 25584_C|T, 25683_T|C, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ284784


Target: 27 samples Number of changes: 149
BC: KP.2.3 + XEC.4.1.4 + KP.2.3BC BR: 3-4, 7-8 BC BR coord: 241 - 242, 2789 - 2790
Direction L1: << Initial region span: 1-3,5-7,8-149Gap history (edge excluded): 3-8 -> 3-5
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 4.80e-01
Rec. model vs L1: 5.44e-09 Rec. model vs L2: 1.90e-51
Flags: Model_2BP_Best

KP.2.3 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 3 3.778452 None None None * * *
|||||

XEC.4.1.4 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
XEC.4.1.4 23 5 11.000655 NaN NaN NaN * * *
XEC.13 30 5 11.000655 1.000655 5.998691 1.0 * *
XEC.32 42 5 11.000655 1.000655 5.998691 1.0 * *
XEC.8.1 12 5 11.000655 1.000655 5.998691 1.0 * *
XEC.18.3 13 5 11.000655 1.000655 5.998691 1.0 * *
XEC.18.2 10 5 11.000655 1.000655 5.998691 1.0 * *
XEC.17 13 5 11.000655 1.000655 5.998691 1.0 * *
XEC.16 23 5 11.000655 1.000655 5.998691 1.0 * *
XEC.4.7 13 5 11.000655 1.000655 5.998691 1.0 * *
XEC.35.1 28 5 11.000655 1.000655 5.998691 1.0 * *
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 8 177.246779 NaN NaN NaN * * *
KP.3.1.1 12013 5 174.719309 177.550075 -37.100151 3.096183e-02 *
KP.3 769 8 170.987129 175.600349 -33.200698 4.405066e-03 * *
KP.3.3 1715 5 170.138538 168.366230 -18.732459 3.175644e-06
KP.2 1589 8 168.951364 173.609055 -29.218110 6.021524e-04 * *
XEC.32 42 5 167.115100 158.104405 1.791191 1.111656e-10
KP.3.1 1957 5 164.156223 165.619134 -13.238267 2.040298e-07
XEC.14 193 6 163.084371 157.250667 3.498666 4.727687e-11
JN.1 17255 8 162.512873 165.522859 -13.045717 1.855391e-07 *
JN.1.16.1 466 8 162.165099 166.493511 -14.987022 4.894419e-07 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 375_A|G, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T,
9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16173_C|T, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T,
21765_21770, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C,
22578_G|A, 22594_C|T, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A,
22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C,
23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T,
25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C,
28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ286973


Target: 27 samples Number of changes: 149
BC: JN.1.16.1 + KP.3.3.10 BC BR: 129-130 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-129,132-149Gap history (edge excluded): 129-132
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.63e-19 Rec. model vs L2: 1.14e-33
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 129 172.578324 NaN NaN NaN * * *
XEC.32 42 147 167.785198 160.017457 -34.034915 3.492125e-06
MC.24.1 25 129 166.419119 166.419119 -46.838238 2.112253e-03 * *
XEC.39 155 129 165.916189 165.916189 -45.832379 1.274757e-03 * *
KP.3 769 129 165.747551 165.747551 -45.495103 1.080858e-03 * *
KP.3.1.1 12013 149 165.604646 159.220535 -32.441069 1.576978e-06
KP.3.3 1715 129 164.503789 164.503789 -43.007578 3.112233e-04 * *
XEC.14 193 129 161.700616 161.700616 -37.401232 1.883112e-05 * *
KP.2 1589 137 160.360936 160.095924 -34.191849 3.782974e-06
XEC.8 592 147 155.612318 146.105693 -6.211385 3.177266e-12
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 132 21.967750 NaN NaN NaN * * *
XEC.2.2 273 132 19.186886 -0.813114 45.626228 6.172909e-02 * *
XEC.32 42 132 19.087602 -0.912398 45.824796 5.613476e-02 * *
KP.3.1.1 12013 131 16.384112 6.384112 31.231776 8.268184e+01 * *
LP.8.1 1124 132 15.415830 -4.584170 53.168340 1.422983e-03 * *
JN.1.11.1 226 139 12.160138 -8.318174 60.636348 3.397111e-05 *
KR.1.4 24 146 10.910774 -33.066710 110.133420 6.088255e-16
XEC.8 592 131 10.694884 0.694884 42.610233 2.794310e-01 * *
XEC.2 921 131 10.238426 0.238426 43.523149 1.772844e-01 * *
XEC.17 13 132 9.123188 -10.876812 65.753625 2.639292e-06 *



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G,
9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C,
17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20914_A|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770,
21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C,
22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G,
22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G,
23423_C|T, 23525_C|T, 23557_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T,
26270_C|T, 26529_G|C, 26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27323_C|T, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T,
28291_C|A, 28311_C|T, 28362_28370, 28600_T|C, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ288044


Target: 27 samples Number of changes: 146
BC: JN.1.16.1 + KP.3.3.10 BC BR: 127-128 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-127,135-146Gap history (edge excluded): 127-135
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.61e-19 Rec. model vs L2: 1.77e-40
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 127 178.279539 NaN NaN NaN * * *
KP.3.3 1715 144 177.577207 169.847037 -53.694074 2.171331e-04 *
XEC.16 23 144 172.335345 164.532019 -43.064037 1.067704e-06
XEC.39 155 144 170.406722 162.642357 -39.284713 1.613000e-07
MC.24.1 25 144 168.792999 162.297526 -38.595051 1.148085e-07
KP.2.3 4440 133 167.817671 158.350575 -30.701150 2.210604e-09
KP.3.1 1957 146 166.569726 157.542921 -29.085842 9.883344e-10
KP.2 1589 127 166.185206 166.185206 -46.370413 5.587380e-06 *
XEC.14 193 144 165.123157 157.646073 -29.292146 1.092278e-09
KP.3.1.1 12013 146 163.310339 157.002670 -28.005340 5.759502e-10
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 135 23.206758 NaN NaN NaN * * *
XEC.2.2 273 135 20.429564 9.186886 23.626228 6.172909e-02 * *
KP.3.1 1957 129 19.026805 9.026805 23.946390 5.260206e-02 *
KP.3.1.1 12013 129 16.307669 6.307669 29.384662 3.482517e-03 *
KR.1.4 24 143 10.910774 -23.066710 88.133420 6.088255e-16
XEC.32 42 135 10.362196 -5.914595 53.829189 1.708611e-08 *
MR.1 17 135 10.362196 -0.876812 43.753625 2.639292e-06 *
XEC.16 23 135 10.362196 -0.876812 43.753625 2.639292e-06 *
MR.2 14 135 10.362196 -0.876812 43.753625 2.639292e-06 *
XEC.17 13 135 10.362196 -0.876812 43.753625 2.639292e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21607_.|GNNNNNNNNNNN, 21618_C|T, 21622_C|T, 21624_G|C, 21627_C|A, 21633_21641, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T,
21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C,
22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22770_G|A, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C,
22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T,
23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C,
26577_C|G, 26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T,
28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ288054


Target: 27 samples Number of changes: 136
BC: JN.1.16.1 + KP.3.3.10 BC BR: 117-118 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-117,125-136Gap history (edge excluded): 117-125
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 3.61e-19 Rec. model vs L2: 9.95e-36
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 117 142.396306 NaN NaN NaN * * *
KP.3.3 1715 134 129.836921 122.106751 35.786497 1.542286e-09
KP.3.1 1957 136 127.271158 118.244353 43.511294 3.249288e-11
KP.2 1589 117 121.319053 121.319053 37.361894 7.034671e-10 *
KP.3.1.1 12013 136 117.671911 111.364242 57.271515 3.340737e-14
MC.24.1 25 134 117.528579 111.033106 57.933789 2.401735e-14
KP.3 769 117 116.660774 116.660774 46.678452 6.659345e-12 *
XEC.16 23 134 114.909623 107.106296 65.787408 4.717889e-16
KP.2.3 4440 123 110.466941 100.999845 78.000310 1.052883e-18
JN.1 17255 117 110.270646 110.270646 59.458708 1.117609e-14 *
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 125 23.206758 NaN NaN NaN * * *
XEC.2.2 273 125 20.429564 9.186886 23.626228 6.172909e-02 * *
KP.3.1 1957 119 19.026805 9.026805 23.946390 5.260206e-02 *
KP.3.1.1 12013 119 16.307669 6.307669 29.384662 3.482517e-03 *
KR.1.4 24 133 10.910774 -23.066710 88.133420 6.088255e-16
XEC.32 42 125 10.362196 -5.914595 53.829189 1.708611e-08 *
MR.1 17 125 10.362196 -0.876812 43.753625 2.639292e-06 *
XEC.16 23 125 10.362196 -0.876812 43.753625 2.639292e-06 *
MR.2 14 125 10.362196 -0.876812 43.753625 2.639292e-06 *
XEC.17 13 125 10.362196 -0.876812 43.753625 2.639292e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T, 10029_C|T,
10198_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G,
18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T,
22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C,
22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G,
23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23629_T|C, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T,
25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C,
27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ288074


Target: 27 samples Number of changes: 146
BC: KP.3.1.1 + LF.7.9 + KP.3.1.1BC BR: 34-35, 49-50 BC BR coord: 12906 - 12907, 21710 - 21711
Direction L1: << Initial region span: 1-34,35-49,50-146Gap history (edge excluded): 34-50 ->
Alt. candidates: [], []
Model 1BP/2BP comparison: 2BP vs 1BP: 9.53e-19
Rec. model vs L1: 1.50e-63 Rec. model vs L2: 3.88e-99
Flags: Model_2BP_Best

KP.3.1.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 34 21.881532 None None None * * *
|||||

LF.7.9 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
LF.7.9 20 35 17.551727 NaN NaN NaN * * *
PY.4 10 37 13.961332 9.541598 38.916805 3.321247e-04 *
PL.1.1 12 48 11.544410 3.156059 51.687881 5.601843e-07
LF.7.1.10 13 48 11.464368 -3.517815 65.035631 7.069932e-10
XFG.2 500 48 11.370057 -6.264129 70.528257 4.542311e-11
LF.7.3.5 16 48 11.256728 -4.542545 67.085090 2.536667e-10
XFJ.1 59 48 11.204542 -4.292347 66.584694 3.273471e-10
PY.2 17 48 11.196104 -4.432754 66.865509 2.831626e-10
XFG.3.1 87 48 11.161286 0.649296 56.701408 4.575339e-08
XFG.3 480 48 10.946573 -4.000604 66.001207 4.374757e-10
|||||

KP.3.1.1 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.1.1 12013 50 143.744428 NaN NaN NaN * * *
PG.3 31 50 140.430068 155.840527 -33.681053 5.628964e-05 * *
KP.2.3 4440 50 139.220879 149.072326 -20.144653 6.460332e-08 *
XEC.32 42 60 136.702794 140.012977 -2.025953 7.546026e-12
KP.3.3.2 217 50 136.312808 126.824332 24.351335 1.410503e-17 *
KP.3.1 1957 48 135.311718 140.362613 -2.725225 1.070832e-11
JN.1 17255 9 132.336765 134.689354 8.621291 3.673671e-14
PG.6 23 50 131.523507 133.621942 10.756115 1.260100e-14 *
KP.3 769 48 126.270755 121.750348 34.499304 8.817178e-20
XEC.2.2 273 60 124.191888 136.003953 5.992094 1.368351e-13



Target sequence

, 21_C|T, 44_C|T, 241_C|T, 515_520, 670_T|G, 897_C|A, 2060_G|A, 2585_2587, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5104_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A,
9344_C|T, 9365_C|T, 9424_A|G, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T,
15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T, 17934_C|A, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20914_A|C, 21641_G|T, 21653_T|C, 21711_C|T, 21765_21770, 21941_G|T, 21987_G|A,
21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T,
22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A,
22992_G|A, 22995_C|A, 23005_T|A, 23009_23011, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G,
23604_C|G, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 25592_A|G, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G,
26610_A|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28362_28370, 28600_T|C,
28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ288105


Target: 27 samples Number of changes: 136
BC: JN.1.16.1 + KP.3.3.10 BC BR: 118-119 BC BR coord: 27263 - 27264
Direction L1: >> Initial region span: 1-118,126-136Gap history (edge excluded): 118-126
Alt. candidates: [], []
Model 1BP/2BP comparison: -
Rec. model vs L1: 4.61e-19 Rec. model vs L2: 7.38e-42
Flags: Model_2BP_Bad_L1_opp

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 118 142.849571 NaN NaN NaN * * *
KP.3.3 1715 134 118.318237 112.080283 51.839433 4.332702e-14
KP.3.1.1 12013 136 116.449369 111.651598 52.696805 2.818462e-14
KP.3.1 1957 136 115.902597 108.292437 59.415126 9.790000e-16
KP.2.3 4440 124 111.447986 101.980890 72.038220 1.779855e-18
KP.2 1589 118 111.386318 111.386318 53.227365 2.162341e-14 *
JN.1 17255 118 109.687913 109.687913 56.624174 3.970041e-15 *
KP.3 769 118 106.659750 106.659750 62.680499 1.918151e-16 *
MC.24.1 25 134 106.139391 101.201324 73.597352 8.158960e-19
JN.1.4 8971 118 105.217185 105.217185 65.565631 4.521965e-17 *
|||||

KP.3.3.10 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.3.3.10 55 126 21.649352 NaN NaN NaN * * *
XEC.2.2 273 126 18.939203 7.696525 26.606951 6.620495e-02 * *
KP.3.1 1957 120 17.610160 7.610160 26.779680 6.081006e-02 *
KP.3.1.1 12013 120 14.797771 4.797771 32.404458 3.661069e-03 *
KR.1.4 24 133 10.910774 -24.624117 91.248234 6.088255e-16
XEK.2 67 126 8.820538 -2.418471 46.836942 2.679179e-06 *
MR.1 17 126 8.804789 -2.434219 46.868439 2.639292e-06 *
XEC.4.7 13 126 8.804789 -2.434219 46.868439 2.639292e-06 *
XEC.32 42 126 8.804789 -7.472002 56.944003 1.717175e-08 *
XEC.17 13 126 8.804789 -2.434219 46.868439 2.639292e-06 *



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9344_C|T, 9365_C|T, 9424_A|G, 9430_C|T, 9534_C|T,
10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A, 16600_T|C, 17410_C|T,
18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 20168_A|C, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T, 22194_22196,
22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T, 22865_G|T,
22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C, 23039_C|G,
23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23629_T|C, 23854_C|A, 23948_G|T, 24378_C|T, 24424_A|T, 24469_T|A, 24872_G|T,
24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27259_A|C, 27321_A|G, 27382_G|C, 27383_A|T,
27384_T|C, 27807_C|T, 27810_T|C, 27828_C|T, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T, 29734_29759

Case 122 (XFN): OZ288128


Target: 27 samples Number of changes: 139
BC: JN.1.16.1 + KP.2.3 BC BR: 44-45 BC BR coord: 21653 - 21654
Direction L1: << Initial region span: 1-43,45-139Gap history (edge excluded): 43-45
Alt. candidates: [], []
Model 1BP/2BP comparison: 1BP vs 2BP: 9.81e-07
Rec. model vs L1: 1.14e-42Rec. model vs L2: 1.43e-25
Flags: Model_1BP_Best

JN.1.16.1 >>

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
JN.1.16.1 466 43 46.216326 NaN NaN NaN * * *
JN.1 17255 43 36.251832 17.494911 85.010178 1.259671e-10 *
XEC.25 13 36 30.934459 -7.590022 135.180043 1.606868e-21
JN.1.7 1974 43 28.153578 10.423381 99.153238 1.071014e-13 *
XEC.17 13 36 27.463722 -11.541015 143.082029 3.093976e-23
KP.3.1.1 12013 32 27.333999 -7.587713 135.175426 1.606868e-21
KP.3.3 1715 36 27.043808 4.468359 111.063282 2.776973e-16
XEC.39 155 36 25.899451 -12.579296 145.158593 1.093580e-23
XEC.16 23 15 24.119754 -24.312403 168.624807 8.801901e-29
XEC.18.3 13 15 24.119754 -32.642224 185.284448 2.122772e-32
|||||

KP.2.3 <<

num_seq t_ch_MAX max_CL CL@BC_t_ch_MAX aic PV PV_OK t_ch_MAX_OK phyl_OK
KP.2.3 4440 45 131.390260 NaN NaN NaN * * *
KP.3.1.1 12013 45 124.322999 124.322999 -40.645999 8.544949e-04 * *
PG.3 31 45 114.960379 114.960379 -21.920757 7.320515e-08 *
KP.3 769 25 107.691914 93.532616 20.934768 3.628962e-17
KP.3.1 1957 25 106.719037 103.805175 0.389649 1.047097e-12
KP.3.3 1715 1 102.447114 97.978754 12.042491 3.091871e-15
XEC.2.2 273 54 98.911785 91.998845 24.002310 7.818805e-18
KP.2 1589 25 97.364066 93.601235 20.797529 3.872679e-17
KP.3.3.10 55 25 97.331456 94.210473 19.579053 7.127400e-17
KP.3.3.2 217 54 96.121273 94.976707 18.046586 1.531674e-16



Target sequence

, 241_C|T, 670_T|G, 897_C|A, 2060_G|A, 2790_C|T, 3037_C|T, 3431_G|T, 3565_T|C, 4184_G|A, 4321_C|T, 5577_T|C, 6183_A|G, 7842_A|G, 8293_C|T, 8393_G|A, 9322_T|C, 9344_C|T, 9365_C|T, 9424_A|G,
9430_C|T, 9534_C|T, 10029_C|T, 10198_C|T, 10228_C|T, 10447_G|A, 10449_C|A, 11042_G|T, 11288_11296, 11727_G|A, 12789_C|T, 12815_C|T, 12880_C|T, 13339_T|C, 14408_C|T, 15714_C|T, 15756_T|A,
16600_T|C, 17410_C|T, 18163_A|G, 18492_A|G, 18894_C|T, 19955_C|T, 20055_A|G, 21653_T|C, 21711_C|T, 21941_G|T, 21987_G|A, 21992_21994, 22032_T|C, 22033_C|A, 22034_A|G, 22107_A|G, 22132_G|T,
22194_22196, 22200_T|G, 22208_C|T, 22295_C|A, 22353_C|A, 22556_A|G, 22577_G|C, 22578_G|A, 22599_G|C, 22629_A|C, 22674_C|T, 22679_T|C, 22686_C|T, 22688_A|G, 22775_G|A, 22786_A|C, 22813_G|T,
22865_G|T, 22882_T|G, 22895_G|C, 22896_T|A, 22898_G|A, 22910_A|G, 22916_C|T, 22917_T|G, 22926_T|C, 22928_T|C, 22942_T|A, 22992_G|A, 22995_C|A, 23005_T|A, 23012_G|A, 23018_T|C, 23019_T|C,
23039_C|G, 23055_A|G, 23063_A|T, 23075_T|C, 23222_G|A, 23271_C|T, 23403_A|G, 23423_C|T, 23525_C|T, 23599_T|G, 23604_C|G, 23854_C|A, 23856_G|T, 23948_G|T, 24058_C|T, 24378_C|T, 24424_A|T,
24469_T|A, 24872_G|T, 24990_C|T, 25000_C|T, 25006_C|T, 25207_C|T, 25584_C|T, 26060_C|T, 26270_C|T, 26529_G|C, 26577_C|G, 26681_C|T, 26709_G|A, 26833_C|T, 26858_C|T, 27059_C|T, 27259_A|C,
27321_A|G, 27382_G|C, 27383_A|T, 27384_T|C, 27807_C|T, 27810_T|C, 28031_T|C, 28271_A|T, 28291_C|A, 28311_C|T, 28881_G|A, 28882_G|A, 28883_G|C, 28884_G|C, 28958_C|A, 29510_A|C, 29543_G|T,
29734_29759